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
//
More information about the Bioperl-l
mailing list