LENGTHSi
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Input sequence is divided into fragments having this length.
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OVERLAP
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Nucleotides shared between 2 consecutive fragments.
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RSITES
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Given a DNA sequence, one signal per RSITES nucleotides is
estimated to be predicted on (computing NUMSITES).
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REXONS
|
Given a DNA sequence, one exon per REXONS nucleotides is estimated
to be predicted on (computing NUMEXONS).
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RBSITES
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Given a DNA sequence, one signal per RBSITES nucleotides is the estimated
ratio of sites which must be copied between 2 fragments
(computing BACKUPSITES).
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RBEXONS
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Given a DNA sequence, one exon per RBEXONS nucleotides is the estimated
ratio of exons which must be copied between 2 fragments
(computing BACKUPEXONS).
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RFIRST
|
NUMEXONS / RFIRST initial exons are supposed to be predicted in LENGTHSi bases.
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RINTER
|
NUMEXONS / RINTER internal exons are supposed to be predicted in LENGTHSi bases.
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RTERMI
|
NUMEXONS / RTERMI terminal exons are supposed to be predicted in LENGTHSi bases.
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RSINGL
|
NUMEXONS / RSINGL single genes are supposed to be predicted in LENGTHSi bases.
|
RORF
|
NUMEXONS / RSINGL ORFs are supposed to be predicted in LENGTHSi bases.
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FSORT
|
FSORT * NUMEXONS is the maximum number of predicted exons (both strands)
in LENGTHSi bases.
|
NUMEVIDENCES
|
Maximum number of annotations per locus
read from optional file.
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MAXHSP
|
Maximum number of HSPs (protein homology) read
from optional file (per locus, strand and frame).
|
MAXNSEQUENCES
|
Maximum number of locus in multi-fasta files.
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MAXGENE
|
Maximum number if predicted genes.
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MAXEXONGENE
|
Maximum amount of exons in every gene.
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MAXAA
|
Maximum length of predicted proteins (in amino acids).
|
MAXCDNA
|
Maximum length of exonic sequence for a gene (cDNA).
|
MAXISOCHORES
|
Maximum number of isochores in the parameters file.
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EXONLENGTH, SINGLEGENELENGTH, ORFLENGTH
|
Minimum allowed size for internal exons, single genes and ORFs.
|
MINEXONLENGTH, MINSCORELENGTH
|
Minimum size for exons to compute protein coding potential (score if not).
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ISOCONTEXT
|
Size of region around an exon when its G+C content is computed.
|
NULL_OLIGO_SCORE
|
Penalty for N's in scoring exons.
|
LOCUSLENGTH
|
Maximum number of chars for the name of the input sequence.
|
OLIGOLENGTH
|
Maximum length for the oligonucleotides used in Markov chains
(scoring sites and exons).
|
VERSION
|
Current geneid version.
|
SITES, EXONS, EVIDENCE
|
Field feature in gff standard.
|
FRAMES, STRANDS, FORWARD, REVERSE, ACC, DON, STA, STO, FIRST,
INTERNAL, TERMINAL, SINGLE, ORF, LENGTHCODON, PERCENT, MEGABYTE,
MAXTIMES, PROT, DNA, MINUTE
|
Numerical constants.
|
sFORWARD, sREVERSE, sACC, sDON, sSTA, sSTO, sFIRST, sINTERNAL,
sTERMINAL, sSINGLE, sORF, sEXON, xmlFORWARD, xmlREVERSE
|
String constants.
|
BLOCK, NONBLOCK
|
Mark gene model rules as blocking or not blocking. To preserve or not
the group structure in gene annotations (evidences).
|
COFFSET
|
Correction because of arrays in C starts from 0 to N -1.
|
MAXLINE
|
Maximum number of characters read from input line.
|
MAXSTRING
|
Maximum allowed length of geneid messages and strings.
|
MAXENTRY, MAXTYPE, MAXINFO, NOTFOUND
|
Dictionary (hash table) definitions.
|
HASHFACTOR
|
Computing size of hash table to save best genes (sites, exons).
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PARAMETERFILE
|
Default parameters file: filename.
|
FILENAMELENGTH
|
Maximum size for filenames.
|
INFI, sINFI, INF
|
Representing the infinity value.
|
MAXSCORE
|
Default value for annotations forced to appear in the final prediction.
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FASTALINE
|
Lenght (maximum) for fasta lines
|
MESSAGE_FREQ
|
Display message with amount of sequence read (frequency).
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NOGROUP
|
String to represent (ab initio) exons without group (field 9 in gff).
|