genewise [was Re: [Bioperl-l] pointer to pseudowise ?]

George Hartzell hartzell at kestrel.alerce.com
Thu Sep 29 17:43:03 EDT 2005


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.

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.

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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