Multiple meta-alignment web server help


Table of contents:
  1. SEQUENCES/MAPS box
  2. ENGINE BEHAVIOUR switch
  3. PARAMETERS definition
  4. MAPPING options
  5. The OUTPUT format
SEQUENCES/MAPS box
This box can contain either a multi FASTA file or a GFF file depending on the value of the switch Engine behaviour:
  1. Mapping and meta-alignment: 
    >M13483
TCCTTACATGGTCTGGGGGCTCCCTGGCTGATCCTCTCCCCTGCCCTTGGCTCCATGAAT
GGCCTCGGCAGTCCTAGCGGGTGCGAAGGGGACCAAATAAGGCAAGGTGGCAGACCGGGC
CCCCCACCCCTGCCCCCGGCTGCTCCAACTGACCCTGTCCATCAGCGTTCTATAAAGCGG
CCCTCCTGGAGCCAGCCACCC...
>M26773
TGTCTGTCCCCTGCAGCCCCAGCCCAGCTGTCAGGACCCTTCTCCAAGGGCAGGGCGCCAAGTCTTCCGG
CATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGACTCATTGTCCCTTAGTTT
GGAAGGGCTGAAGAGCAATAAGCCCACTCCACAACTAGGGAGCTCCCCCACCCAAGGGGCGCATTGGCAT
CACATAGCCTTTCCCCGTCCC...
>galGal2_refGene_NM_001031229 
TTAGCTGGTTTGAAATGATGATGGAGCACATACTATGGACAGTTTCAAAA
CACATGCTGTCCTTGATTGCATTTTAAAGTCAGGATATCATCTTTCTACG
TGCACCAGTCTTGTCAGGATGATAGAGGCAGGGGACATCATACTGAATCT
GATGCAAAAAGACCTTTGTTTTTGCAGCTGTCAGTCCAGCAGTCTTCTTT
...
  2. Only meta-alignment: 
    M13483	MatScan	Myf	24	35	4.31	.	.
M13483	MatScan	Hen-1	27	38	3.41	.	.
M13483	MatScan	Hen-1	27	38	3.56	.	.
M13483	MatScan	Myf	27	38	5.41	.	.
M13483	MatScan	Myf	27	38	6.19	.	.
...
M13483	MatScan	Bsap	477	496	3.91	.	.
M13483	MatScan	NRF-2	479	488	3.80	.	.
M13483	MatScan	NRF-2	480	489	2.95	.	.
M13483	MatScan	RXR-VDR	486	500	4.45	.	.
M26773	MatScan	CFI-USP	2	11	3.41	.	.
M26773	MatScan	COUP-TF	5	18	4.94	.	.
M26773	MatScan	Chop-cEBP	9	20	3.09	.	.
M26773	MatScan	NRF-2	9	18	2.95	.	.
...
M26773	MatScan	TBP	470	484	6.14	.	.
M26773	MatScan	Hen-1	472	483	4.13	.	.
M26773	MatScan	NRF-2	481	490	3.64	.	.
M26773	MatScan	CREB	489	500	2.80	.	.
galGal2_refGene_NM_001031229	MatScan	Pbx	10	21	3.73	.	.
galGal2_refGene_NM_001031229	MatScan	Pbx	17	28	3.95	.	.
galGal2_refGene_NM_001031229	MatScan	HNF-3beta	24	35	3.21	.	.
...
ENGINE BEHAVIOUR:
  1. Mapping and meta-alignment:
    Input nucleotide sequences to predict the TFBSs with one of the available position weight matrices collections and then, produce the meta-alignment of both maps

  2. Only meta-alignment:
    Input the maps (lists of TFBSs in GFF format with "\t" as field separator) to perform the meta-alignment. The TFBSs must be sorted according to their first position in the corresponding sequence.
PARAMETERS:
  1. α favours the presence in the alignment of TFBSs with higher predictive scores.

  2. λ penalizes the number of input elements between two consecutive matches that are not included in the alignment.

  3. μ selects those homologous sites that show similar position conservation in the promoter sequences.

  4. γ is the penalty for introducing a gap in a given column.

  5. c is the penalty for non-collinearity in the alignments.
MAPPING OPTIONS:
  1. Matrix collection:
    Select the collection of position weight matrices to predict the TFBSs

  2. Mapping threshold quality:
    Select the minimum mapping predictive value (1.0 is the best)
OUTPUT FORMATS:
  1. Default format:
    TBP:	 469 470 459 -
    means a TBP factor has been located at 469 in the first map, 470 in the second map,
    459 in the third map. It was not located, however, in the fourth map.

  2. GFF format:
    M13483-OUT	metaM_v1.0	TBP	469	483	.	.	.	TBP
M26773-OUT	metaM_v1.0	TBP	470	484	.	.	.	TBP
danRer3_refGene_NM_214784-OUT	metaM_v1.0	TBP	459	473	.	.	.	TBP
    means exactly the same as before.




Enrique Blanco Garcia © 2006