genewise [was Re: [Bioperl-l] pointer to pseudowise ?]
Jason Stajich
jason.stajich at duke.edu
Thu Sep 29 21:38:18 EDT 2005
On Sep 29, 2005, at 5:43 PM, George Hartzell wrote:
>
> On a related note, now that I have a wise-2.2.3-rc7 which passes it's
> tests, I'm trying Promoterwise.t (which passes, yay!) and Genewise.t
> (which doesn't, sigh...).
>
> The Version string in my version of genewise doesn't return anything
> useful, so the Genewise.t code compares the results to what it has
> stashed for 2.2.3-rc7.
I know, Ewan will fix that before the release.
I assume that without a version that it is 2.2.3-rc7 for testing
purposes.
>
> Oddly enough, the answers that I'm seeing seem to be an amalgam of
> those expect for 2-2-0 and 2.2.3-rc7.
>
There should be an if/elsif in the t/Genewise.t do you have that?
I think I got interrupted before finishing these tests as looks like
I transposed some nums, should pass on both versions now.
> I've included the output from running genewise by hand (as reported by
> running with -verbose => 1).
>
> Anyone see something I'm doing wrong?
>
> g.
>
> genewise $Name: $ (unreleased release)
> This program is freely distributed under a GPL. See source directory
> Copyright (c) GRL limited: portions of the code are from separate
> copyright
>
> Query protein: roa1_drome
> Comp Matrix: BLOSUM62.bla
> Gap open: 12
> Gap extension: 2
> Start/End default
> Target Sequence HSHNRNPA
> Strand: forward
> Start/End (protein) default
> Gene Parameter file: gene.stat
> Splice site model: Position Weight Matrix
> Pseudo counts 5'SS 1.00
> Pseudo counts 3'SS 1.00
> Minimum SS collar -5.00
> Maximum SS collar 5.00
> Splice site offset 1.50
> Codon Table: codon.table
> Subs error: 1e-06
> Indel error: 1e-06
> Null model syn
> Algorithm 623
>
> genewise output
> Score 319.10 bits over entire alignment
> Scores as bits over a synchronous coding model
>
> Warning: The bits scores is not probablistically correct for single
> seqs
> See WWW help for more info
>
> roa1_drome 26 EPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDVV
> EPE +RKLFIGGL + TTDE+L++HFE+WG + D V
> EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV
> HSHNRNPA 1386 gcgccaactaggtatgaaggacaactgctgacagtg
> acaatgatttggtgtaccaagtggataaggctcagt
> gcaggggcctaggctaattgcggcttgagagcgctg
>
>
> roa1_drome 62 VMKDPRTKRSRGFGFITYSHSS
> VM+DP TKRSRGFGF+TY+
> VMRDPNTKRSRGFGFVTYATVE
> HSHNRNPA 1494 GTAAGAT Intron 1 CAGgaagcaaactagtgtgatgagg
> <0-----[1494 : 1788]-0>ttgacacagcggtgttcaccta
> agataccgctgctgtcatctgg
>
>
> roa1_drome 84 MIDEAQKSRPHKIDGRVVEPKRAVPRQ
> +D A +RPHK+DGRVVEPKRAV R+
> EVDAAMNARPHKVDGRVVEPKRAVSRE
> HSHNRNPA 1855 gggggaagaccagggagggcaaggtag
> atacctacgcaataggttacagctcga
> ggtatgtagacggtaatgaagatccaa
>
>
> roa1_drome 111 DIDSPNAGATVKKLFVGALKDD
> D P A TVKK+FVG +K+D
> DSQRPGAHLTVKKIFVGGIKED
> HSHNRNPA 1936 GTGAGTG Intron 2 TAGgtcacggctagaaatgggaagg
> <0-----[1936 : 2083]-0>acagcgcatctaatttggtaaa
> ttaaatccatgagatttctaac
>
>
> roa1_drome 133 HDEQSIRDYFQHFGNIVDINIVIDKETGKKRGFAFVEFDDYDPVDKVV
> +E +RDYF+ +G I I I+ D+ +GKKRGFAFV FDD+D VDK+V
> TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV
> HSHNRNPA 2150 aggcccagttgctgaaggagaaagcgagaaagtgtgatggcgtggaag
> caaaatgaataaagatattattcaggggaaggtcttctaaaactaatt
> taatcaatttagtaatagtacgtcactcgagctctactcctccgtgtc
>
>
> roa1_drome 181 QKQHQLNGKMVDVKKALP
> QK H +NG +V+KAL
> L:I[att] QKYHTVNGHNCEVRKALS
> HSHNRNPA 2294 AGTAAGTA Intron 3 TAGTTcatcagagcatggaagct
> <1-----[2295 : 2387]-1> aaaactagaagatgactc
> gacttgtccctataacga
>
>
> roa1_drome 200 QN
> Q
> K:N[aac] QR
> HSHNRNPA 2444 AAGCAAGAG Intron 4 CAGCca
> <2-----[2446 : 2472]-2> ag
> aa
>
>
> roa1_drome 203 QQGGGGGRGGPGGRAGGNR
> + G G GG GG GGN
> D:G[ggt] RSGSGNFGGGRGGGFGGND
> HSHNRNPA 2480 GGTATGCT Intron 5 AAGGTcagtgatgggcgggtggag
> <1-----[2481 : 2566]-1> gggcgatgggggggtggaa
> atttactttttattctgtc
>
>
> roa1_drome 223 GNMGGGNYGNQN GGGNWNN
> GGN+ + GG +
> NFGRGGNFSGRG -:I[ata] GGFGGSR
> HSHNRNPA 2626 atgcggatagcgATGTATGGT Intron 6 TACAggtggac
> atggggatgggg <2-----[2664 : 2791]-2> ggtgggg
> ccttaacctttt tcttcct
>
>
> roa1_drome 242 GGNNWGNNRGGNDNWGNN F
> GG +G + G + +GN+
> GGGGYGGSGDGYNGFGND S:G[gga] S
> HSHNRNPA 2814 ggggtggagggtagtgagGGTAAGTT Intron 7 GAGGAa
> ggggaggggagaagtgaa <1-----[2869 : 3108]-1> g
> tttattctgtcttatctt c
>
>
> roa1_drome 262 GGGGGGGGGYGGGNNSWGNNNPWD--NGNGGGNFGGGG
> G G GG GYG + +G + +D N GGG FGGG
> RGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGGFGGGS
> HSHNRNPA 3114 agtgaggcgtgacgagtggagatgataagggggtggga
> ggaggggagagaagggagggggaagaaagggggtgggg
> actattagttacgctctcgtcctcctccacacctcttt
>
>
> roa1_drome 298 NNWNNGG--NDFGGYQ-QN
> N+ GG NDFG Y Q+
> -:G[gga] SNFGGGGSYNDFGNYNNQS
> HSHNRNPA 3228 GGTAGGTA Intron 8 TAGGAaatggggatagtgataact
> <1-----[3229 : 3805]-1> gatgggggaaatgaaaaac
> cttattacctttgtcctgt
>
>
> roa1_drome 314 YGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQ
> GP +GG NF PY GGG + A NQ
> SNFGPMKGG-NFGGRSSGPYGGGGQYFAKPRNQ
> HSHNRNPA 3865 tatgcaagg atggaatgctggggcttgaccac
> catgctagg atggggcgcaggggaatcacgaa
> attacggaa ttacactcctctacactaaaaca
>
>
> roa1_drome 347 NYGGNNQGFNNGGNNRRY
> YGG++ + G+ RR+
> G:G[ggt] GYGGSSSS-SSYGSGRRF
> HSHNRNPA 3961 GGTATGGT Intron 9 CAGGTgtggtaaa aatgagaat
> <1-----[3962 : 4251]-1> gaggcggg ggagggggt
> ctctcccc tctctcaat
>
>
> //
> Gene 1
> Gene 1386 4304
> Exon 1386 1493 phase 0
> Supporting 1386 1493 26 61
> Exon 1789 1935 phase 0
> Supporting 1789 1935 62 110
> Exon 2084 2294 phase 0
> Supporting 2084 2293 111 180
> Exon 2388 2445 phase 1
> Supporting 2390 2443 182 199
> Exon 2473 2480 phase 2
> Supporting 2474 2479 201 202
> Exon 2567 2663 phase 1
> Supporting 2569 2661 204 234
> Exon 2792 2868 phase 2
> Supporting 2793 2867 235 259
> Exon 3109 3228 phase 1
> Supporting 3111 3185 261 285
> Supporting 3192 3227 286 297
> Exon 3806 3961 phase 1
> Supporting 3808 3828 298 304
> Supporting 3835 3855 305 311
> Supporting 3859 3891 312 322
> Supporting 3892 3960 324 346
> Exon 4252 4304 phase 1
> Supporting 4254 4277 348 355
> Supporting 4278 4304 357 365
> //
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>
--
Jason Stajich
Duke University
http://www.duke.edu/~jes12
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