Utilities

General tools

• html2txt.c

this C program reads as standard input an HTML file and generates as standard output a text with all HTML tags removed and  a quite conserved layout. This program is used as a filter to extract prediction data from HTML documents generated by some prediction software available on the Web.
• cutInGene.pl realData predData

This program takes as input parameters a real data set file made of contigs, and a standardized output of a prediction software. The purpose of the program is to split the predicted exons in numbered sets corresponding to real partition in genes (deduced from the real data set). A correspondance.txt file is generated which gives the new numbering of the entries.

Automation

• NetStart 1.0 (netstart.pl)

This program needs two parameters: the location of a folder containing all needed FASTA files*, and a Data.list file.
Foreach contig in Data.list, il will submit the sequence to NetStart, thist for both strands. The ouput of NetStart is filtered with html2txt. The resulting prediction data are stored in the current directory a file whose name looks like seq##start#.txt (where ## is the contig number and # is 1 or 2 depending on the strand -normal or reverse -).
Output of this program are used by start2st.pl.
• SplicePredictor (sp_reformat.pl)

This program takes as first parameter a splice predictor output file and direct or reverse as second parameter. It splits the input files into two files for each sequence (one for each strand).  The name of output file follows the following format: seq##splicep#.txt where ## is the contig number and # is 1 for direct strand or 2 for reverse strand.
• Genefinder-SPL (spl.pl)

This program takes the same king of parameters as the one for NetStart.  The output files have names which look like seq##spl#.txt where ## is the contig number and # is 1 for direct strand or 2 for reverse strand.
• Genefinder-FEX (fex.pl)

This program takes the same king of parameters as the one for NetStart.  The output files have names which look like seq##fex#.txt where ## is the contig number and # is 1 for direct strand or 2 for reverse strand.
• Genefinder-Fgenea (fgenea.pl)

This program takes the same king of parameters as the one for NetStart.  The output files have names which look like seq##fgene#.txt where ## is the contig number and # is 1 for direct strand or 2 for reverse strand.
• Genefinder-Fgenep (fgenep.pl)

This program takes the same king of parameters as the one for NetStart.  The output files have names which look like seq##fgene#.txt where ## is the contig number and # is 1 for direct strand or 2 for reverse strand.
• MZEF (mzef.pl)

This program takes the same king of parameters as the one for NetStart,plus two optional parameter settings: overlap=xxx and prior_proba=yyy (default values for overlap and prior_proba are respectively 0 and .03).  The output files have names which look like seq##mzef#.txt where ## is the contig number and # is 1 for direct strand or 2 for reverse strand.
• Grail (xGrail.pl)

This program takes the same king of parameters as the one for NetStart.  The output files have names which look like seq##grail.txt where ## is the contig number.
• GeneMark.hmm (GeneMarkHMM.pl)

This program takes the same king of parameters as the one for NetStart. In addition to html2txt filter, this program use also  GMHMMreformat.pl perl script.The output files have names which look like seq##gmhmm.txt where ## is the contig number.

1. name of FASTA sequence files MUST START with seq## (where ## is the contig number on 2 digits) and have .tfa as file extension (ie: seq01ac002332g14g15.tfa)
2. a Data.list file is a text file which contains per line the name of a contig (ie: seq01) and the length of the sequence, separated by a tabulation.

If you encounter a problem, contact Patrice Déhais