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Note, the Algorithms described in algo.html by Jim helps understanding these files.

Input data files -> processing programs -> outputs:

Input File(s)
Processing program Output file(s)
./cDNA/allcdna.cdi Probably from GenBank flat files or via Entrez browser
./features/sanger/syn Obtained possibly from Lincoln Stein
./features/celegans.syn Obtained possibly from Lincoln Stein
./nt4/*.dna.gz fatont4 ./nt4/*.nt4
./cDNA/allcdna.fa indexfa ./cDNA/allcdna.ix
./?/*.gff geniegff ./features/sanger/c2g ./features/sanger/genes.gdf
./genie/*.gff geniegff ./features/genie/c2g ./features/genie/genes.gdf
./features/c2c makepgo ./features/*.coo
./cDNA/allcdna.ix refiAli ./ga/good.txt ./ra/bad.txt ./ra/cool.txt
./ga/good.txt binGood ./cDNA/good.ali
./cDNA/good.ali ali2alx ./cDNA/*.alx
./ra/good.txt cdnaOff ./cDNA/*.cdo>
./ra/good.txt introns cDNA/introns.gff cDNA/introns.txt obsolete/altintron.txt $(html_root)/intronerator/altsplice.raw.html cDNA/introns.fa
./cDNA/good.ali ixali ./cDNA/good.ix
./ra/good.txt $(html_root)/intronerator/nameless.raw.html cluster ./features/c2g
./features/c2g ixword3 ./features/c2g.ix
./features/c2c ixword3 ./features/c2c.ix
./features/sanger/genes.gdf indexgl ./features/sanger/genes.ix
./features/c2g makepgo ./features/sanger/*.pgo
./features/sanger/genes.gdf indexgl ./features/sanger/genes.ix
./features/c2c makepgo ./features/*.coo
./features/genie/c2g makepgo ./features/genie/*.pgo
./features/sanger/syn ./features/syn moresyn ./features/orf2gene ./features/orfInfo
./xeno/cbriggsae/ ixxenost ./xeno/cbriggsae/all.ix
./xeno/cbriggsae/ stToXao ./xeno/cbriggsae/*.xao

Annotations for files in interonerator/idb

./makefile - looks like most files here are created by processes specified in this makefile
./README - brief listing of several files in cDNA, ra/good.txt and xeno/cbriggsae/
./makefile.bak - garbage
./ea/ - compressed all.out file - results of alignments
./nt4/i.nt4 - Are these 2-bit-a-base representations of DNA from lib/nt4.c ?
./nt4/ii.nt4 - by processing the dna.gz files below ?
./nt4/I.dna.gz - these dna.gz are the C. elegans chromosomes
./nt4/III.dna.gz - This nt4 directory is an argument to refiAli in the makefile
./nt4/IV.dna.gz - which specifies chromDir
./cDNA/ - I assume this directory is the C. elegans data
./cDNA/allcdna.ix - the .ix files are indexes to the .fa files
./cDNA/allcdna.fa - created by indexfa
./cDNA/introns.fa - list of introns in fa format, created by introns
./cDNA/good.ali - a binary version of ga/good.txt created by binGood
./cDNA/i.alx - .alx index files created from good.ali via the ali2alx program
./cDNA/i.cdo - .cdo - cDNA offsets created from ra/good.txt via cdnaOff program
./cDNA/ii.cdo - cdnaOff creates an index for each chromosome from ra/good.txt
./cDNA/iii.alx - ali2alx creates an index for each chromsome from good.ali
./cDNA/introns.gff - the intron feature file listing, see also  GFF_Spec  - created by introns
./cDNA/introns.txt - list of introns in GFF format, created by introns
./cDNA/allcdna.cdi - looks like these are from genBank to cDNA info file format via gb2cdi, see gb2cdi.c for field format
./ra/good.txt - each and every cDNA alignment described - the output of a run of refiAli (refineAli.c)
./ra/bad.txt.gz - from the output of refiAli, scores too low
./ra/cool.txt.gz - from the output of refiAli, unusual features
./features/c2c - looks like a list of identified features in sorted order by their coordinates
./features/c2c.ix - created by ixword3 from c2c
./features/i.coo - from makepgo run on c2c file - predicted gene offset files 
./features/ii.coo - I can't find the difference between .coo and .pgo
./features/c2g - A cluster listing from sanger/c2g and ra/good.txt, from the output of cluster
./features/c2g.ix - created by ixword3 from c2g
./features/celegans.syn - A synonyms table, from where ?
./features/syn - Synonyms table
./features/orfInfo - info of ORFs, created by moresyn from the syn table
./features/orf2gene - orf to gene table, created by moresyn from syn table
./features/sanger/c2g - feature list from the sanger viewpoint ?
./features/sanger/genes.gdf - Genie gene predictions, From Sanger ?
./features/sanger/genes.ix - created by indexgl from genes.gdf
./features/sanger/i.pgo - predicted Gene Offset - from makepgo working on c2g
./features/sanger/syn - A synonyms table, from Sanger ?
./features/genie/genes.gdf - Genie gene predictions, from genie/*.gff
./features/genie/c2g - a cluster listing, from what features ?
./features/genie/i.pgo - predicted gene offset files, via makepgo working on c2g
./features/genie/genes.ix - from indexgl operating on genes.gdf
./genie/I.gff - The chromosomes feature files, defines CDS, what is CDS ?
./genie/II.gff - This says  CDS is a cDNA ? 
./xeno/cbriggsae/ - cross species alignment file short stitched, from what ? filtRep.c maybe ?  What data ?
./xeno/cbriggsae/all.ix - index created by ixxenost from
./xeno/cbriggsae/i.xao - index files from
./foo - temporary shell file garbage
./trash/ - 29 Mb of trash, perhaps temp files used by the browser ?

This page last updated: Tuesday, 30-Mar-2010 12:06:39 PDT.