.gptot { float: left; } .gptoc { border: 1px solid #009F9F; vertical-align: top; /* float: left; */ } .geneid { float: left; margin: 0px; margin-top: 5px; margin-left: 10px; width: 380px; } .sgp { float: left; margin: 0px; margin-top: 5px; margin-left: 10px; width: 380px; } .gpset { border: 1px dotted black; margin-top: 5px; } EOH; # function makenewset() { # USAGE: # $genome=<<'; $preds=hrefs($BASE_URL.'/'.$preds,'Follow this link'); echo <<
Genome Version:$genome
$program Version:$version
Parameter File:$param
Predictions Set:$preds
EOT; echo ''; } # makenewset # function makenewpwset() { # USAGE: # $Qspecies=''; # $Qgenome=<<'; $preds=hrefs($BASE_URL.'/'.$preds,'Follow this link'); echo <<
Genome Versions: <$Qspecies> $Qgenome
<$Tspecies> $Tgenome
$program Version$version
Parameter File:$param
Predictions Set:$preds
EOT; echo ''; } # makenewpwset # function sorry() { global $program; echo "

Sorry, no $program results
available for this species.

"; } # sorry # the_header('Precomputed Gene Predictions on Whole Genome Sequences', 'geneid, gene prediction, genome sequence annotation, gene prediction on genomic sequences, computational gene annotation, golden path, ensembl, human genome, chimp genome, rat genome, mouse genome, fly genome, fungal genomes', 'PRECOMPUTED GENE PREDICTIONS on WHOLE GENOME SEQUENCES',$add_style); ?>

The predictions available on this page have been obtained by using the gene-finding software geneid and SGP2. SGP2 combines geneid predictions with tblastx comparison of a query genome from one species (i.e. human) against an informant genome of another species (i.e. from mouse).

Available precomputed whole-genome prediction data sets:

Vertebrates

Homo sapiens','HSAPIENS', csli('geneid','HSAPgeneid', 'SGP2 : Human vs Mouse','HSAPsgpmouse', 'SGP2 : Human vs Rat', 'HSAPsgprat'),'' ),'', # HSAPIENS cstxt('Rattus norvegicus','RNORVEGICUS', csli('geneid','RNORgeneid', 'SGP2 : Rat vs Human','RNORsgp'),'' ),'', # RNORVEGICUS cstxt('Mus musculus','MMUSCULUS', csli('geneid','MMUSgeneid', 'SGP2 : Mouse vs Human','MMUSsgp'),'' ),'', # RNORVEGICUS cstxt('Bos taurus','BTAURUS', csli('geneid','BTAUgeneid', 'SGP2 : Cow vs Mouse','BTAUsgp'),'' ),'' # BTAURUS ); ?>
Gallus gallus','GGALLUS', csli('geneid','GGALgeneid', 'SGP2 : Chicken vs Human','GGALsgphuman', 'SGP2 : Chicken vs Cow','GGALsgpcow', 'SGP2 : Chicken vs Human+Cow','GGALsgp'),'' ),'', # GGALLUS 'Pan troglodytes','PTROGLODYTES', cstxt('Felis catus','FCATUS', csli('geneid','FCATgeneid', 'SGP2 : Cat vs Mouse','FCATsgp'),'' ),'', # FCATUS cstxt('Equus caballus','ECABALLUS', csli('geneid','ECABALLUSgeneid', 'SGP2 : Horse vs Mouse','ECABALLUSsgp'),'' ),'', # ECABALLUS cstxt('Macaca mulatta','MMULATTA', csli('geneid','MMULATTAgeneid', 'SGP2 : Rhesus Monkey vs Mouse','MMULATTAsgp'),'' ),'', # MMULATTA 'Cavia porcellus','CPORCELLUS', 'Loxodonta africana','LAFRICANA', 'Oryctolagus cuniculus','OCUNICULUS', 'Dasypus novemcinctus','DNOVEMCINCTUS', 'Echinops telfairi','ETELFAIRI', 'Petromyzon marinus','PMARINUS', 'Branchiostoma floridae','BFLORIDAE', 'Tetraodon nigroviridis','TNIGROVIRIDIS' ); ?>

Invertebrates

Drosophila melanogaster','DMELANOGASTER', 'Drosophila simulans','DSIMULANS', 'Drosophila mojavensis','DMOJAVENSIS', 'Drosophila pseudoobscura','DPSEUDOOBSCURA', 'Drosophila ananassae','DANANASSAE', 'Drosophila yakuba','DYAKUBA', 'Drosophila virilis','DVIRILIS', 'Anopheles gambiae','AGAMBIAE', 'Apis mellifera','AMELLIFERA', 'Caenorhabditis elegans','CELEGANS' ); ?>

Forthcoming

Fugu rubripes','FRUBRIPES', 'Dictyostelium discoideum','DDISCOIDEUM' ); ?>

 

Homo sapiens','HSAPIENS'); ################################ ?>
'.$program.'','HSAPgeneid'); ## $genome=<<goldenPath. December 2013 hg38 human genome assembly (GRCh38). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.4.'; $param='human3iso.param'; $preds='H.sapiens/hg38/geneid_v1.4'; makenewset(); ## $genome=<<goldenPath. March 2006 hg19 human genome assembly (GRCh37). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.3.'; $param='human3iso.param'; $preds='H.sapiens/golden_path_200902/geneid_v1.3/'; makenewset(); ## $genome=<<goldenPath. March 2006 hg18 human genome assembly (NCBI Build 36). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.2.'; $param='human3iso20060220.param'; $preds='H.sapiens/golden_path_200603/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath. May 2004 hg17 human genome assembly (NCBI Build 35). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.2.'; $param='human3iso.param'; $preds='H.sapiens/golden_path_200405/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath. July 2003 hg16 human genome assembly (NCBI Build 34). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_200307/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath. April 2003 hg15 human genome assembly (NCBI Build 33). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20030410/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (November 14, 2002). November 2002 hg13 human genome assembly (NCBI Build 31). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20021114/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (June 28, 2002). June 2002 hg12 human genome assembly (NCBI Build 30). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20020628/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (April 5, 2002). April 2002 hg11 human genome assembly (NCBI Build 29). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20020405/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (December 22, 2001). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20011222/geneid_v1.1/'; makenewset(); ## $genome=<<Ensembl 8_30 (September 2, 2002). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/ensembl_8_30/geneid_v1.1/'; makenewset(); ## $genome=<<Ensembl 7_29 (July 1, 2002). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/ensembl_4_28/geneid_v1.1/'; makenewset(); ## $genome=<<Ensembl 4_28 (March 7, 2002). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='H.sapiens/ensembl_4_28/geneid_v1.1/'; makenewset(); ## ?>

 

'.$program.' : Human vs Rat ','HSAPsgprat'); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg15, April 2003). EOH; $Tspecies='Rat'; $Tgenome=<<goldenPath (rnJun2003, June, 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg15) against the Rat genome (rn3.1). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20030410_x_rat3.1/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg15, April 2003). EOH; $Tspecies='Rat'; $Tgenome=<<goldenPath (rnJan2003, January, 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg15) against the Rat genome (rn2.1). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20030410_x_rat2003/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg13, November 14, 2002). EOH; $Tspecies='Rat'; $Tgenome=<<goldenPath (rnJan2003, January, 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg15) against the Rat genome (rn2.1). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20021114_x_rat2003/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg12, June 28, 2002). EOH; $Tspecies='Rat'; $Tgenome=<<goldenPath (rnNov2002, November, 2002).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg12) against the Rat genome (rn2.0). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20020628_x_rat/SGP/'; makenewpwset(); ## ?>
'.$program.' : Human vs Mouse ','HSAPsgpmouse'); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg38, December 2013). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm10, December 2011).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg38) against the Mouse genome (mm10). EOH; $version='geneid version_1.4'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/hg38_x_mm10/SGP'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg19, February 2009). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm9, July 2007).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg19) against the Mouse genome (mm9). EOH; $version='geneid version_1.3'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/golden_path_200902_x_mm9/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg18, March 2006). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm9, July 2007).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg18) against the Mouse genome (mm9). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/golden_path_200603_x_mm9/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg18, March 2006). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm8, March 2006).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg18) against the Mouse genome (mm8). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/golden_path_200603_x_mm8/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg18, March, 2006). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm7, Aug 2005).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg18) against the Mouse genome (mm7). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/golden_path_200603/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg17, May 2004). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm7, Aug 2005).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg17) against the Mouse genome (mm7). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/golden_path_200405_x_mm7/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg17, May 2004). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm6, March 2005).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg17) against the Mouse genome (mm6). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/golden_path_200405_x_mm6/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg17, May 2004). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm5, May 2004).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg17) against the Mouse genome (mm5). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='H.sapiens/golden_path_200405/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg16, July 2003). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm4, November 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg16) against the Mouse genome (mm4). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_200307_x_mm4/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg16, July 2003). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (February, 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg16) against the Mouse genome (mm3.1). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_200307/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg15, April 2003). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (February, 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg15) against the Mouse genome (mm3.1). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20030410/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg13, November 14, 2002). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (February, 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg13) against the Mouse genome (mm3.1). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20021114/SGP_mm2003/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg13, November 14, 2002). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (February, 2002).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg13) against the Mouse genome (mm3). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20021114/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (hg12, June 28, 2002). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (February, 2002).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome (hg12) against the Mouse genome (mm3). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='/H.sapiens/golden_path_20020628/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (December 22, 2001). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (February, 2002).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome against the Mouse genome. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20011222/SGP/'; makenewpwset(); ## $Qspecies='Human'; $Qgenome=<<goldenPath (August 6, 2001). EOH; $Tspecies='Mouse'; $Tgenome=<<sanger_phusion_20011109 (9th of November 2001).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Human genome against the Mouse genome. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='H.sapiens/golden_path_20010806/SGP/'; makenewpwset(); ## ?>

 

Mus musculus','MMUSCULUS'); ################################ ?>
'.$program.'','MMUSgeneid'); ## $genome=<<goldenPath (mm10, Dec 2011). Predictions were obtained on the masked version of the genome. These are the predictions for the mm10 version of the mouse genome assembly. EOH; $version='version_1.4'; $param='human3iso.param'; $preds='M.musculus/mm10/geneid_v1.4'; makenewset(); ## $genome=<<goldenPath (mm9, July 2007). Predictions were obtained on the masked version of the genome. These are the predictions for the mm9 version of the mouse genome assembly. EOH; $version='version_1.2'; $param='human3iso20060220.param'; $preds='M.musculus/mmJul2007/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath (mm8, March 2006). Predictions were obtained on the masked version of the genome. These are the predictions for the mm8 version of the mouse genome assembly. EOH; $version='version_1.2'; $param='human3iso20060220.param'; $preds='M.musculus/mmMar2006/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath (mm7, August 2005). Predictions were obtained on the masked version of the genome. These are the predictions for the mm7 version of the mouse genome assembly. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='M.musculus/mmDec2005/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath (mm6, March 2005). Predictions were obtained on the masked version of the genome. These are the predictions for the mm6 version of the mouse genome assembly. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='M.musculus/mmMar2005/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath (mm5, May 2004). Predictions were obtained on the masked version of the genome. These are the predictions for the mm5 version of the mouse genome assembly. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='M.musculus/mmMay2004/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath (mm4, November 2003). Predictions were obtained on the masked version of the genome. These are the predictions for the mm4 version of the mouse genome assembly. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmOct2003/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (February, 2003). Predictions were obtained on the masked version of the genome. These are the predictions for the mm3.1 version of the mouse genome assembly. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2003/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (February, 2002). Predictions were obtained on the masked version of the genome. These are the predictions for the mm2 version of the mouse genome assembly. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2002/geneid_v1.1/'; makenewset(); ## $genome=<<Ensembl 5_3 (1st of May 2002). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='M.musculus/ensembl_5_3/geneid_v1.1/'; makenewset(); ## $genome=<<Ensembl 4_1 (7th of March 2002). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='M.musculus/ensembl_4_1/geneid_v1.1/'; makenewset(); ## ?>
'.$program.' : Mouse vs Human ','MMUSsgp'); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm10, Dec 2011). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. December 2013 hg38 human genome assembly.
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm10) against the Human genome (hg38). EOH; $version='geneid version_1.4'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mm10/SGP2/hg38'; makenewpwset(); ## ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm9, July 2007). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. March 2006 hg18 human genome assembly (NCBI Build 36).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm9) against the Human genome (hg18). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mmJul2007/SGP/humangp200603/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm8, March 2006). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. March 2006 hg18 human genome assembly (NCBI Build 36).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm8) against the Human genome (hg18). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mmMar2006/SGP/humangp200603/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm7, August 2005). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. March 2006 hg18 human genome assembly (NCBI Build 36).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm7) against the Human genome (hg18). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mmDec2005/SGP/humangp200603/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm7, August 2005). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. May 2004 hg17 human genome assembly (NCBI Build 35).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm7) against the Human genome (hg17). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mmDec2005/SGP/humangp200405/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm6, March 2005). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. May 2004 hg17 human genome assembly (NCBI Build 35).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm6) against the Human genome (hg17). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mmMar2005/SGP/humangp200405/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm5, May 2004). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. May 2004 hg17 human genome assembly (NCBI Build 35).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm5) against the Human genome (hg17). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mmMay2004/SGP/humangp200405/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (mm4, November 2003). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. July 2003 hg16 human genome assembly (NCBI Build 34).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm4) against the Human genome (hg16). EOH; $version='geneid version_1.1'; $param='human3iso.sgp.Hs-Mm.param'; $preds='M.musculus/mmOct2003/SGP/humangp200307/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (February, 2003). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. April 2003 hg15 human genome assembly (NCBI Build 33).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm3.1) against the Human genome (hg15). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2003/SGP/humangp20030410/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (February, 2003). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (November 14, 2002). November 2002 hg13 human genome assembly (NCBI Build 31).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm3.1) against the Human genome (hg13). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2003/SGP/humangp20021114/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (February, 2002). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (November 14, 2002). November 2002 hg13 human genome assembly (NCBI Build 31).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome (mm3) against the Human genome (hg13). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2002/SGP/humangp20021114/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (February, 2002). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (28th of June 2002). June 2002 hg12 human genome assembly (NCBI Build 30).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Mouse genome (mm3) against the Human genome (hg12). EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2002/SGP/humangp20020628'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (February, 2002). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (22nd of December 2001).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Mouse genome against the Human genome. NOTE: For SGP-evid predictions, coordinates of RefSeq genes were considered so that SGP2 (geneid) would not make any predictions in those regions. This allows for SGP2 to make predictions between already known (RefSeq) genes with higher accuracy. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2002+evid/SGP/'; makenewpwset(); ## $Qspecies='Mouse'; $Qgenome=<<goldenPath (February, 2002). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (22nd of December 2001).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the mouse genome against the Human genome. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='M.musculus/mmFeb2002/SGP/humangp20011222/'; makenewpwset(); ## ?>

 

Rattus norvegicus','RNORVEGICUS'); ################################ ?>
'.$program.'','RNORgeneid'); ## $genome=<<goldenPath (rnJul2014). Predictions were obtained on the masked version of the genome. These are the predictions for the Jul 2014 version (rn4) of the rat genome assembly. EOH; $version='version_1.4'; $param='human3iso.param'; $preds='R.norvegicus/rn6/geneid_v1.4'; makenewset(); ## $genome=<<goldenPath (rnNov2004, Nov, 2004). Predictions were obtained on the masked version of the genome. These are the predictions for the Nov 2004 version (rn4) of the rat genome assembly. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='R.norvegicus/rnNov2004/geneid_v1.2/'; makenewset(); ## $genome=<<goldenPath (rnJun2003, June, 2003). Predictions were obtained on the masked version of the genome. These are the predictions for the Jun 2003 version (3.1) of the rat genome assembly. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='R.norvegicus/rnJun2003/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (rnJan2003, January, 2003). Predictions were obtained on the masked version of the genome. These are the predictions for the Jan2003 version (2.1) of the rat genome assembly. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='R.norvegicus/rnJan2003/geneid_v1.1/'; makenewset(); ## $genome=<<goldenPath (rnNov2002, November, 2002). Predictions were obtained on the masked version of the genome. These are the predictions for the Nov2002 version (2.0) of the rat genome assembly. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='R.norvegicus/rnNov2002/geneid_v1.1/'; makenewset(); ## ?>
'.$program.' : Rat vs Human ','RNORsgp'); ## $Qspecies='Rat'; $Qgenome=<<goldenPath (rnJul2014). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. Dec 2013 hg38 human genome assembly.
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Rat genome (rn6) against the Human (hg38) genome. EOH; $version='geneid version_1.4'; $param='human3iso.sgp.Hs-Mm.param'; $preds='R.norvegicus/rn6/SGP2/hg38'; makenewpwset(); ## $Qspecies='Rat'; $Qgenome=<<goldenPath (rnNov2004, November, 2004). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. March 2006 hg18 human genome assembly (NCBI Build 36).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Rat genome (rn4) against the Human (hg18) genome. EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm.param'; $preds='R.norvegicus/rnNov2004/SGP/humangp200603'; makenewpwset(); ## $Qspecies='Rat'; $Qgenome=<<goldenPath (rnJun2003, June, 2003). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (April 10, 2003). Predictions were obtained on the masked version of both genomes. tblastx comparison of the Rat genome against the Human genome. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='R.norvegicus/rnJun2003/SGP/humangp20030410'; makenewpwset(); ## $Qspecies='Rat'; $Qgenome=<<goldenPath (rnJan2003, January, 2003). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (10th of April 2003).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Rat genome against the Human genome. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='R.norvegicus/rnJan2003/SGP/humangp20030410'; makenewpwset(); ## $Qspecies='Rat'; $Qgenome=<<goldenPath (rnJan2003, January, 2003). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (November 14, 2002).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Rat genome against the Human genome. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='R.norvegicus/rnJan2003/SGP/humangp20021114'; makenewpwset(); ## $Qspecies='Rat'; $Qgenome=<<goldenPath (rnNov2002, November, 2002). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (June 28, 2002).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Rat genome against the Human genome. EOH; $version='geneid version_1.1'; $param='human3iso.param'; $preds='R.norvegicus/rnNov2002/SGP/humangp20020628'; makenewpwset(); ## ?>

 

Gallus gallus','GGALLUS'); ################################ ?>
'.$program.'','GGALgeneid'); ## $genome=<<goldenPath (February, 2004). Predictions were obtained on the masked version of the genome. These are the predictions for the Feb.2004 version of the Chicken genome assembly produced at the Genome Sequencing Center at Washington University in St. Louis. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='G.gallus/golden_path_200402/geneid_v1.1/'; makenewset(); ## ?>

 

'.$program.' : Chicken vs Human ','GGALsgphuman'); ## $Qspecies='Chicken'; $Qgenome=<<goldenPath (February, 2004). These are the predictions for the Feb.2004 version of the Chicken genome assembly produced at the Genome Sequencing Center at Washington University in St. Louis. EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. May 2004 hg17 human genome assembly (NCBI Build 35).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Chicken genome (ggalFeb2004) against the Human genome (hg17). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Gg-Hs.param'; $preds='G.gallus/golden_path_200402/SGP/humangp200405'; makenewpwset(); ## $Qspecies='Chicken'; $Qgenome=<<goldenPath (February, 2004). These are the predictions for the Feb.2004 version of the Chicken genome assembly produced at the Genome Sequencing Center at Washington University in St. Louis. EOH; $Tspecies='Human'; $Tgenome=<<goldenPath. July 2003 hg16 human genome assembly (NCBI Build 34).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Chicken genome (ggalFeb2004) against the Human genome (hg16). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Gg-Hs.param'; $preds='G.gallus/golden_path_200402/SGP/humangp200307'; makenewpwset(); ## ?>
'.$program.' : Chicken vs Human+Cow ','GGALsgp'); ## $Qspecies='Chicken'; $Qgenome=<<goldenPath (February, 2004). Predictions were obtained on the masked version of the genome. These are the predictions for the Feb.2004 version of the Chicken genome assembly produced at the Genome Sequencing Center at Washington University in St. Louis. EOH; $Tspecies='Cow + Human'; $Tgenome=<< Cow: goldenPath (Btau2, March 2005).
Human: goldenPath (hg17-ncbi 35-May 2004).
NOTE: These SGP2 predictions combine geneid predictions with tblastx comparison of the Chicken genome (ggalFeb2004) against the Human and Cow genomes (SRs -similarity regions- i.e. homology evidences from both species to G.gallus were combined). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Gg-Bt_Hs.param'; $preds='G.gallus/golden_path_200402/SGP/humangp200405+Btau2'; makenewpwset(); ## ?>

 

'.$program.' : Chicken vs Cow ','GGALsgpcow'); ## $Qspecies='Chicken'; $Qgenome=<<goldenPath (February, 2004). These are the predictions for the Feb.2004 version of the Chicken genome assembly produced at the Genome Sequencing Center at Washington University in St. Louis. EOH; $Tspecies='Cow'; $Tgenome=<<goldenPath (Btau2, March 2005).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Chicken genome (ggalFeb2004) against the Cow genome (Btau2). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Gg-Bt.param'; $preds='G.gallus/golden_path_200402/SGP/Btau2'; makenewpwset(); ## ?>

 

Pan troglodytes','PTROGLODYTES'); ################################ ?>
'.$program.'','PTROgeneid'); ## $genome=<<goldenPath (November, 2003). Predictions were obtained on the masked version of the genome. These are the predictions for the Nov. 13 2003 version of the ARACHNE assembly of the chimpanzee genome, produced by the Chimpanzee Sequencing Consortium. EOH; $version='version_1.1'; $param='human3iso.param'; $preds='P.troglodytes/golden_path_200311/geneid_v1.1/'; makenewset(); ## ?>
'.$program.'','PTROsgp'); ## sorry(); ## ?>

 

Felis catus','FCATUS'); ################################ ?>
'.$program.'','FCATgeneid'); ## $genome=<<goldenPath (March, 2006). Predictions were obtained on the masked version of the genome. These are the predictions for the March 2006 version of the BROAD release 3 assembly of the cat genome, produced by the Broad Institute. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='F.catus/golden_path_200603/geneidv1.2'; makenewset(); ## ?>
'.$program.' Cat vs Mouse ','FCATsgp'); ## $Qspecies='Cat'; $Qgenome=<<goldenPath (felCat3, March 2006). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm8, March, 2006).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Cat (felCat3) genome against the Mouse genome (mm8). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Bt_NEW.param'; $preds='F.catus/golden_path_200603/SGP/200603mm8/'; makenewpwset(); ## ?>

 

Equus caballus','ECABALLUSgeneid'); ################################ ?>
'.$program.'','ECABALLUSgeneid'); ## $genome=<<goldenPath (equCab1, January, 2007). Predictions were obtained on the masked version of the genome. These are the predictions for the January 2007 version of the BROAD assembly of the horse genome, produced by the Broad Institute. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='E.caballus/ecJan2007/geneid_v1.2'; makenewset(); ## ?>
'.$program.' Horse vs Mouse ','ECABALLUSsgp'); ## $Qspecies='Horse'; $Qgenome=<<goldenPath (equCab1, January 2007). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm8, March, 2006).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Horse (equCab1) genome against the Mouse genome (mm8). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm_NEW.param'; $preds='E.caballus/ecJan2007/SGP/200603mm8/'; makenewpwset(); ## ?>

 

Macaca mulatta','MMULATTA'); ################################ ?>
'.$program.'','MMULATTAgeneid'); ## $genome=<<goldenPath (rheMac2, January, 2006). Predictions were obtained on the masked version of the genome. These are the predictions for the January 2006 version of the Baylor assembly of the rhesus monkey genome, produced by the Baylor College of Medicine Human Genome Sequencing Center. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='M.mulatta/rmJan2006/geneid_v1.2'; makenewset(); ## ?>
'.$program.' Rhesus Monkey vs Mouse ','MMULATTAsgp'); ## $Qspecies='Monkey'; $Qgenome=<<goldenPath (rheMac2, January, 2006). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (mm8, March, 2006).
Predictions were obtained on the masked version of both genomes. tblastx comparison of the Monkey (rheMac2) genome against the Mouse genome (mm8). EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Mm_NEW.param'; $preds='M.mulatta/rmJan2006/SGP/200603mm8'; makenewpwset(); ## ?>

 

Cavia porcellus','CPORCELLUS'); ################################ ?>
'.$program.'','CPORgeneid'); ## $genome=<<goldenPath (February, 2008). Predictions were obtained on the masked version of the genome. These are the predictions for the Feb 2008 assembly of the guinea pig genome (cavPor3) obtained from the Broad Institute. EOH; $version='version_1.3'; $param='human3iso.param'; $preds='C.porcellus/golden_path_200806/geneidv1.3/'; makenewset(); ## ?>
'.$program.'','CPORsgp'); ## sorry(); ## ?>

 

Loxodonta africana','LAFRICANA'); ################################ ?>
'.$program.'','LAFRgeneid'); ## $genome=<<goldenPath (May, 2005). Predictions were obtained on the masked version of the genome. These are the predictions for the May 2005 assembly of the elephant genome (loxAfr1) obtained from the Broad Institute. EOH; $version='version_1.2'; $param='human3iso20060220.param'; $preds='L.africana/golden_path_200505/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','LAFRsgp'); ## sorry(); ## ?>

 

Oryctolagus cuniculus','OCUNICULUS'); ################################ ?>
'.$program.'','OCUNgeneid'); ## $genome=<<goldenPath (May, 2005). Predictions were obtained on the masked version of the genome. These are the predictions for the May 2005 assembly of the rabbit genome (oryCun1) obtained from the Broad Institute. EOH; $version='version_1.2'; $param='human3iso20060220.param'; $preds='O.cuniculus/golden_path_200505/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','OCUNsgp'); ## sorry(); ## ?>

 

Dasypus novemcinctus','DNOVEMCINCTUS'); ################################ ?>
'.$program.'','DNOVgeneid'); ## $genome=<<goldenPath (May, 2005). Predictions were obtained on the masked version of the genome. These are the predictions for the May 2005 assembly of the armadillo genome (dasNov1) obtained from the Broad Institute. EOH; $version='version_1.2'; $param='human3iso20060220.param'; $preds='D.novemcinctus/golden_path_200505/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','DNOVsgp'); ## sorry(); ## ?>

 

Echinops telfairi','ETELFAIRI'); ################################ ?>
'.$program.'','ETELgeneid'); ## $genome=<<goldenPath (July, 2005). Predictions were obtained on the masked version of the genome. These are the predictions for the July 2005 assembly of the tenrec genome (echTel1) obtained from the Broad Institute. EOH; $version='version_1.2'; $param='human3iso20060220.param'; $preds='E.telfairi/golden_path_200507/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','ETELsgp'); ## sorry(); ## ?>

 

Petromyzon marinus','PMARINUS'); ################################ ?>
'.$program.'','PMARgeneid'); ## $genome=<<goldenPath (March, 2007). Predictions were obtained on the masked version of the genome. These are the predictions for the March 2007 assembly of the lamprey genome (petMar1) obtained from the Genome Sequencing Center at the Washington University School of Medicine in St. Louis. EOH; $version='version_1.3'; $param='human3iso20060220.param'; $preds='P.marinus/golden_path_200806/geneidv1.3'; makenewset(); ## ?>
'.$program.'','DNOVsgp'); ## sorry(); ## ?>

 

Branchiostoma floridae','BFLORIDAE'); ################################ ?>
'.$program.'','BFLOgeneid'); ## $genome=<<goldenPath (March, 2006). Predictions were obtained on the masked version of the genome. These are the predictions for the March 2006 assembly of the lancelet genome (braFlo1) obtained from the US DOE Joint Genome Institute (JGI). EOH; $version='version_1.3'; $param='human3iso20060220.param'; $preds='B.floridae/golden_path_200806/geneidv1.3/'; makenewset(); ## ?>
'.$program.'','PMARsgp'); ## sorry(); ## ?>

 

Bos taurus','BTAURUS'); ################################ ?>
'.$program.'','BTAUgeneid'); ## $genome=<<goldenPath (Dec 2009). Predictions were obtained on the masked version of the genome. These are the predictions for the December 2009 Cow genome assembly (bosTau8) produced by the Baylor College of Medicine Human Genome Sequencing Center. EOH; $version='version_1.4'; $param='human3iso.param'; $preds='B.taurus/bosTau8/geneid_v1.4'; makenewset(); ## $genome=<<hgsc (August, 2006). Predictions were obtained on the masked version of the genome. These are the predictions for the August 2006 Cow genome assembly (bosTau3) produced by the Baylor College of Medicine Human Genome Sequencing Center. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='B.taurus/hgsc_Btau20060815/geneidv1.2/'; makenewset(); ## $genome=<<goldenPath (March, 2005). Predictions were obtained on the masked version of the genome. These are the predictions for the March 2005 Cow genome assembly (bosTau2) produced by the Baylor College of Medicine Human Genome Sequencing Center. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='B.taurus/golden_path_200503/geneidv1.2/'; makenewset(); ## $genome=<<goldenPath (September, 2004). Predictions were obtained on the masked version of the genome. These are the predictions for the September 2004 Cow genome assembly (bosTau1) produced by the Baylor College of Medicine Human Genome Sequencing Center. EOH; $version='version_1.2'; $param='human3iso.param'; $preds='B.taurus/golden_path_200409/geneidv1.2/'; makenewset(); ## ?>
'.$program.' : Cow vs Human (or Mouse) ','BTAUsgp'); ## $Qspecies='Cow'; $Qgenome=<<hgsc (December, 2009). EOH; $Tspecies='Human'; $Tgenome=<<goldenPath (December, 2013). Predictions obtained on the masked version of both genomes.
tblastx comparison of the Human genome against the Cow (Btau8) genome. EOH; $version='geneid version_1.4'; $param='human3iso.sgp.Hs-Bt.param'; $preds='B.taurus/bosTau8/SGP2/hg38'; makenewpwset(); ## $Qspecies='Cow'; $Qgenome=<<hgsc (August, 2006). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (July, 2007). Predictions obtained on the masked version of both genomes.
tblastx comparison of the Mouse genome against the Cow (Btau3) genome. EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Bt.param'; $preds='B.taurus/hgsc_Btau20060815/SGP/mm9'; makenewpwset(); ## $Qspecies='Cow'; $Qgenome=<<hgsc (August, 2006). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (March, 2006). Predictions obtained on the masked version of both genomes.
tblastx comparison of the Mouse genome against the Cow (Btau3) genome. EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Bt.param'; $preds='B.taurus/hgsc_Btau20060815/SGP/mm8'; makenewpwset(); ## $Qspecies='Cow'; $Qgenome=<<goldenPath (March, 2005). EOH; $Tspecies='Mouse'; $Tgenome=<<goldenPath (March, 2005). Predictions obtained on the masked version of both genomes.
tblastx comparison of the Mouse genome against the Cow (Btau2) genome. EOH; $version='geneid version_1.2'; $param='human3iso.sgp.Hs-Bt.param'; $preds='B.taurus/golden_path_200503/SGP/mm6/'; makenewpwset(); ## ?>

 

Drosophila melanogaster','DMELANOGASTER'); ################################ ?>
'.$program.'','DMELgeneid'); ## $genome=<<goldenPath (April 2004). Release 4 (Apr. 2004, UCSC version dm2) assembly of the Drosophila melanogaster genome. Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='D.melanogaster/golden_path_200404/geneidv1.2/'; makenewset(); ## $genome=<<Ensembl 4_3 (7th of March 2002). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.1'; $param='dros.param'; $preds='D.melanogaster/ensembl_4_3/geneid_v1.1/'; makenewset(); ## ?>
'.$program.'','DMELsgp'); ## sorry(); ## ?>

 

Drosophila simulans','DSIMULANS'); ################################ ?>
'.$program.'','DSIMgeneid'); ## $genome=<<goldenPath Apr. 2005 freeze of the D. simulans genome (droSim1) from the Genome Sequencing Center at Washington University School of Medicine in St. Louis. Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='D.simulans/golden_path_200504/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','DSIMsgp'); ## sorry(); ## ?>

 

Drosophila mojavensis','DMOJAVENSIS'); ################################ ?>
'.$program.'','DMOJgeneid'); ## $genome=<<goldenPath. Drosophila mojavensis 11 August 2004 assembly from Agencourt. Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='D.mojavensis/golden_path_200408/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','DMOJsgp'); ## sorry(); ## ?>

 

Drosophila pseudoobscura','DPSEUDOOBSCURA'); ################################ ?>
'.$program.'','DPSEgeneid'); ## $genome=<<goldenPath. Drosophila pseudoobscura Flybase Release 1.0 assembly (Nov. 2004). Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='D.pseudoobscura/golden_path_200411/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','DPSEsgp'); ## sorry(); ## ?>

 

Drosophila ananassae','DANANASSAE'); ################################ ?>
'.$program.'','DANAgeneid'); ## $genome=<<goldenPath. Drosophila ananassae 15 July 2004 assembly from TIGR. Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='D.ananassae/golden_path_200407/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','DANAsgp'); ## sorry(); ## ?>

 

Drosophila yakuba','DYAKUBA'); ################################ ?>
'.$program.'','DYAKgeneid'); ## $genome=<<goldenPath. Apr. 2004 freeze of the D. yakuba genome (droYak1) from the Genome Sequencing Center at Washington University School of Medicine in St. Louis. Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='D.yakuba/golden_path_200404/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','DYAKsgp'); ## sorry(); ## ?>

 

Drosophila virilis','DVIRILIS'); ################################ ?>
'.$program.'','DVIRgeneid'); ## $genome=<<goldenPath. Drosophila virilis 12 July 2004 assembly from Agencourt Bioscience Corporation. Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='D.virilis/golden_path_200407/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','DVIRsgp'); ## sorry(); ## ?>

 

Anopheles gambiae','AGAMBIAE'); ################################ ?>
'.$program.'','AGAMgeneid'); ## $genome=<<goldenPath. Feb. 2003 assembly of the A. gambiae genome (anoGam1) from the International Anopheles Genome Project (version MOZ2). Predictions were obtained on the masked version of the genome. EOH; $version='version_1.2'; $param='drosophilaENS.param'; $preds='A.gambiae/golden_path_200302/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','AGAMsgp'); ## sorry(); ## ?>

 

Apis mellifera','AMELLIFERA'); ################################ ?>
'.$program.'','AMELLgeneid'); ## $genome=<<goldenPath. Jan. 2005 assembly of the A. mellifera genome (apiMel2) from the Baylor College of Medicine HGSC Honey Bee Genome Project. Predictions were obtained on the unmasked version of the genome. EOH; $version='version_1.2'; $param='BeeENS.param'; $preds='A.mellifera/golden_path_200501/geneidv1.2/'; makenewset(); ## ?>
'.$program.'','AMELLsgp'); ## sorry(); ## ?>

 

Tetraodon nigroviridis','TNIGROVIRIDIS'); ################################ ?>
'.$program.'','TNIGgeneid'); ## $genome=<<tetNig1 (February 2004). February 2004 freeze of the Tetraodon nigroviridis version 7 (V7) genome assembly (UCSC version tetNig1) provided by Genoscope. Predictions were obtained on the masked version of the genome. EOH; $version='version_1.2'; $param='tetramarkov4d.param'; $preds='T.nigroviridis/tetNigFeb2004/geneid_v1.2/'; makenewset(); ## ?>
'.$program.'','TNIGsgp'); ## sorry(); ## ?>

 

Caenorhabditis elegans','CELEGANS'); ################################ ?>
'.$program.'','CELEgeneid'); ## $genome=<<WS120 (March 2004). C. elegans version WS120 deposited into Wormbase as of 1 March 2004. Predictions were obtained on the masked version of the genome. EOH; $version='version_1.2'; $param='celegans1.2.param'; $preds='C.elegans/Ce200403/geneid_v1.2/'; makenewset(); ## ?>
'.$program.'','CELEsgp'); ## sorry(); ## ?>

 

Fugu rubripes','FRUBRIPES'); ################################ ?>
'.$program.'','FRUBgeneid'); ## sorry(); ## ?>
'.$program.'','FRUBsgp'); ## sorry(); ## ?>

 

Dictyostelium discoideum','DDISCOIDEUM'); ################################ ?>
'.$program.'','DDISgeneid'); ## sorry(); ## ?>
'.$program.'','DDISsgp'); ## sorry(); ## ?>