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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