Fwd: Re: [Bioperl-l] Boxes and features...
Lincoln Stein
lstein at cshl.org
Fri Mar 7 14:35:26 EST 2003
For some reason, bioperl-l thinks the headers on this message are suspicious.
So I will forward as an enclosure.
Lincoln
---------- Forwarded Message ----------
Subject: Re: [Bioperl-l] Boxes and features...
Date: Fri, 7 Mar 2003 13:09:56 -0500
From: Lincoln Stein <lstein at cshl.org>
To: "William Boileau" <boileau at essi.fr>, <bioperl-l at bioperl.org>
Hi,
Most likely you are trying to fetch a tag from the arrow feature that you use
as the scale at the top of the picture. You should first check that the tag
exists before you attempt to call it, or you can use the primary_tag to
distinguish between different feature types. The enclosed examples show you
what to do.
Lincoln
On Thursday 06 March 2003 09:27 am, William Boileau wrote:
> Hi,
>
> I tried to remove the box_subparts option (the hit is what I need, not
> each HSP), but it doesn't seem to work.I still have the error "MSG: asking
> for tag value that does not exist name" I didn't try to add the tag to each
> oh the HSPs, but now I hesitate... How can I do that ? for the moment I add
> each HSP to the feature, but how can i add tags to an HSP ?
> Thanks for your answers ! (and I know I owe you much :) )
>
> William
>
> > Hi William,
> >
> > Sorry I didn't notice this before. The problem is that you are using
> > the -box_subparts option when you add the track. This is telling the
> > track to return the SUBFEATURES when you call boxes() rather than the
> > top level features. So what you're getting from boxes() is the HSP
> > subcomponents, which don't happen to have tags.
> >
> > You can either:
> >
> > 1) remove -box_subparts (or set it to 0)
> > 2) add the tags to each of the HSPs
> >
> > It depends on whether you want clicks to be directed at each HSP or at
> > the hit as a whole.
> >
> > Lincoln
> >
> >> >> my $track = $panel->add_track(-glyph => 'graded_segments',
> >> >> -label => 1,
> >> >> -connector => 'dashed',
> >> >> -bgcolor => 'blue',
> >> >> -font2color => 'red',
> >> >> -sort_order => 'high_score',
> >> >> -box_subparts => 1,
> >> >> -description => sub {
> >> >> my $feature = shift;
> >> >> return unless $feature->has_tag('desription');
> >
> > ========================================================================
> > Lincoln D. Stein Cold Spring Harbor
> > Laboratory lstein at cshl.org Cold Spring Harbor, NY
> > ========================================================================
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
--
========================================================================
Lincoln D. Stein Cold Spring Harbor Laboratory
lstein at cshl.org Cold Spring Harbor, NY
========================================================================
-------------------------------------------------------
--
========================================================================
Lincoln D. Stein Cold Spring Harbor Laboratory
lstein at cshl.org Cold Spring Harbor, NY
========================================================================
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hit:
description Human non-histone chromatin protein HMG1 (HMG1) gene, complete cds.
name U51677
hit:
description Mus musculus (clone Clebp-1) high mobility group 1 protein (HMG-1)
name L38477
hit:
description M.musculus HMG1 gene
name X80457
hit:
description Mus musculus HMG-1 mRNA, complete cds.
name U00431
hit:
description Human non-histone chromosomal protein (HMG-1) retropseudogene.
name L08048
hit:
description Human mRNA for high mobility group-1 protein (HMG-1).
name X12597
hit:
description Rat amphoterin mRNA, complete cds.
name M64986
hit:
description M.musculus mRNA for non-histone chromosomal high-mobility group 1
name Z11997
hit:
description Human mRNA for HMG-1, complete cds.
name D63874
hit:
description Human DNA sequence from BAC 445C9 on chromosome 22q12.1.
name Z95115
hit:
description Bovine mRNA for high mobility group 1 (HMG1) protein
name X12796
hit:
description Bovine high-mobility-group protein (HMG-1) mRNA, 3' end.
name M26110
hit:
description Mus musculus HMG-like protein (Trf) mRNA, complete cds.
name AF009343
hit:
description Pig nonhistone protein HMG1 mRNA, complete cds.
name M21683;M21684
hit:
description Homo sapiens (clone 06) high mobility group 1 protein mRNA
name L13805
hit:
description Human chromosomal protein HMG1 related gene.
name D14718
hit:
description Chinese hamster HMG-1 gene for high mobility group protein 1
name Y00365
hit:
description Rat high mobility group 1 protein synthetic gene, complete cds.
name M63852
hit:
description Rat mRNA for high mobility group protein HMG1
name Y00463
hit:
description M.musculus HMG1-R-227 gene
name X80466
hit:
description M.musculus HMG1-R-154 gene
name X80462
hit:
description M.musculus HMG1-R-145 gene
name X80461
hit:
description M.musculus HMG1-R-177 gene
name X80459
hit:
description M.musculus HMG1-R-87 gene
name X80467
hit:
description M.musculus HMG1-R-168 gene
name X80465
hit:
description M.musculus HMG1-R-159 gene
name X80463
hit:
description Rainbow trout HMG-1 gene exons 2-5, complete cds.
name L32859
hit:
description M.musculus HMG1-R-135 gene
name X80460
hit:
description M.musculus HMG1-R-161 gene
name X80464
hit:
description Trout mRNA for high mobility group protein HMG-T
name X02666
hit:
description Xenopus laevis high mobility group protein-1 (HMG-1) mRNA, complete
name U21933
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BLASTN 2.2.1 [Apr-13-2001]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query=
(1500 letters)
Database: Homo_sapiens.cdna.fa
27,628 sequences; 54,878,749 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
ENST00000001380 Gene:ENSG00000000938 Clone:AL031729 Contig:AL031... 2974 0.0
ENST00000311414 Gene:ENSG00000000938 Clone:AL031729 Contig:AL031... 2712 0.0
ENST00000217351 Gene:ENSG00000101371 Clone:AL133293 Contig:AL133... 147 4e-34
ENST00000229471 Gene:ENSG00000010810 Clone:AL158035 Contig:AL158... 96 1e-18
ENST00000229470 Gene:ENSG00000010810 Clone:Z97989 Contig:Z97989.... 96 1e-18
ENST00000012102 Gene:ENSG00000010810 Clone:Z97989 Contig:Z97989.... 96 1e-18
ENST00000262651 Gene:ENSG00000101336 Clone:AL353092 Contig:AL353... 86 1e-15
ENST00000259089 Gene:ENSG00000136573 Clone:AF131216 Contig:AF131... 62 2e-08
ENST00000261799 Gene:ENSG00000113721 Clone:AC005895 Contig:AC005... 46 0.001
ENST00000292410 Gene:ENSG00000160867 Clone:AC027314 Contig:AC027... 44 0.004
ENST00000292408 Gene:ENSG00000160867 Clone:AC027314 Contig:AC027... 44 0.004
ENST00000265442 Gene:ENSG00000105976 Clone:AC002080 Contig:AC002... 42 0.017
ENST00000276497 Gene:ENSG00000147507 Clone:AC046176 Contig:AC046... 40 0.067
ENST00000266054 Gene:ENSG00000107566 Clone:AL138921 Contig:AL138... 40 0.067
ENST00000253055 Gene:ENSG00000130758 Clone:AC118344 Contig:AC118... 40 0.067
>ENST00000001380 Gene:ENSG00000000938 Clone:AL031729
Contig:AL031729.16.1.125287 Chr:1 Basepair:27512639
Status:known
Length = 2350
Score = 2974 bits (1500), Expect = 0.0
Identities = 1500/1500 (100%)
Strand = Plus / Plus
Query: 1 gggaggaccccaatctaggcccaagagggaaagccacgtgcctgtatgagcgtatgagca 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 gggaggaccccaatctaggcccaagagggaaagccacgtgcctgtatgagcgtatgagca 60
Query: 61 tgtgcatgcgcgtgtgtgcacagggtggtgcacctggcaggggtccttgagtgaggcatg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 tgtgcatgcgcgtgtgtgcacagggtggtgcacctggcaggggtccttgagtgaggcatg 120
Query: 121 ccccattctgtagcagggaacctggaatgggctgtgtgttctgcaagaaattggagccgg 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ccccattctgtagcagggaacctggaatgggctgtgtgttctgcaagaaattggagccgg 180
Query: 181 tggccacggccaaggaggatgctggcctggaaggggacttcagaagctacggggcagcag 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tggccacggccaaggaggatgctggcctggaaggggacttcagaagctacggggcagcag 240
Query: 241 accactatgggcctgaccccactaaggcccggcctgcatcctcatttgcccacatcccca 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 accactatgggcctgaccccactaaggcccggcctgcatcctcatttgcccacatcccca 300
Query: 301 actacagcaacttctcctctcaggccatcaaccctggcttccttgatagtggcaccatca 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 actacagcaacttctcctctcaggccatcaaccctggcttccttgatagtggcaccatca 360
Query: 361 ggggtgtgtcagggattggggtgaccctgttcattgccctgtatgactatgaggctcgaa 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 ggggtgtgtcagggattggggtgaccctgttcattgccctgtatgactatgaggctcgaa 420
Query: 421 ctgaggatgacctcaccttcaccaagggcgagaagttccacatcctgaacaatactgaag 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 ctgaggatgacctcaccttcaccaagggcgagaagttccacatcctgaacaatactgaag 480
Query: 481 gtgactggtgggaggctcggtctctcagctccggaaaaactggctgcattcccagcaact 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 gtgactggtgggaggctcggtctctcagctccggaaaaactggctgcattcccagcaact 540
Query: 541 acgtggcccctgttgactcaatccaagctgaagagtggtactttggaaagattgggagaa 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 541 acgtggcccctgttgactcaatccaagctgaagagtggtactttggaaagattgggagaa 600
Query: 601 aggatgcagagaggcagctgctttcaccaggcaacccccagggggcctttctcattcggg 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 601 aggatgcagagaggcagctgctttcaccaggcaacccccagggggcctttctcattcggg 660
Query: 661 aaagcgagaccaccaaaggtgcctactccctgtccatccgggactgggatcagaccagag 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 661 aaagcgagaccaccaaaggtgcctactccctgtccatccgggactgggatcagaccagag 720
Query: 721 gcgatcatgtgaagcattacaagatccgcaaactggacatgggcggctactacatcacca 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 721 gcgatcatgtgaagcattacaagatccgcaaactggacatgggcggctactacatcacca 780
Query: 781 cacgggttcagttcaactcggtgcaggagctggtgcagcactacatggaggtgaatgacg 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 781 cacgggttcagttcaactcggtgcaggagctggtgcagcactacatggaggtgaatgacg 840
Query: 841 ggctgtgcaacctgctcatcgcgccctgcaccatcatgaagccgcagacgctgggcctgg 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 841 ggctgtgcaacctgctcatcgcgccctgcaccatcatgaagccgcagacgctgggcctgg 900
Query: 901 ccaaggacgcctgggagatcagccgcagctccatcacgctggagcgccggctgggcaccg 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 901 ccaaggacgcctgggagatcagccgcagctccatcacgctggagcgccggctgggcaccg 960
Query: 961 gctgcttcggggatgtgtggctgggcacgtggaacggcagcactaaggtggcggtgaaga 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 961 gctgcttcggggatgtgtggctgggcacgtggaacggcagcactaaggtggcggtgaaga 1020
Query: 1021 cgctgaagccgggcaccatgtccccgaaggccttcctggaggaggcgcaggtcatgaagc 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1021 cgctgaagccgggcaccatgtccccgaaggccttcctggaggaggcgcaggtcatgaagc 1080
Query: 1081 tgctgcggcacgacaagctggtgcagctgtacgccgtggtgtcggaggagcccatctaca 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1081 tgctgcggcacgacaagctggtgcagctgtacgccgtggtgtcggaggagcccatctaca 1140
Query: 1141 tcgtgaccgagttcatgtgtcacggcagcttgctggattttctcaagaacccagagggcc 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1141 tcgtgaccgagttcatgtgtcacggcagcttgctggattttctcaagaacccagagggcc 1200
Query: 1201 aggatttgaggctgccccaattggtggacatggcagcccaggtagctgagggcatggcct 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1201 aggatttgaggctgccccaattggtggacatggcagcccaggtagctgagggcatggcct 1260
Query: 1261 acatggaacgcatgaactacattcaccgcgacctgagggcagccaacatcctggttgggg 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1261 acatggaacgcatgaactacattcaccgcgacctgagggcagccaacatcctggttgggg 1320
Query: 1321 agcggctggcgtgcaagatcgcagactttggcttggcgcgtctcatcaaggacgatgagt 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1321 agcggctggcgtgcaagatcgcagactttggcttggcgcgtctcatcaaggacgatgagt 1380
Query: 1381 acaacccctgccaaggttccaagttccccatcaagtggacagccccagaagctgccctct 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1381 acaacccctgccaaggttccaagttccccatcaagtggacagccccagaagctgccctct 1440
Query: 1441 ttggcagattcaccatcaagtcagacgtgtggtcctttgggatcctgctcactgagctca 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1441 ttggcagattcaccatcaagtcagacgtgtggtcctttgggatcctgctcactgagctca 1500
>ENST00000311414 Gene:ENSG00000000938 Clone:AL031729
Contig:AL031729.16.1.125287 Chr:1 Basepair:27512639
Status:known
Length = 2060
Score = 2712 bits (1368), Expect = 0.0
Identities = 1368/1368 (100%)
Strand = Plus / Plus
Query: 133 gcagggaacctggaatgggctgtgtgttctgcaagaaattggagccggtggccacggcca 192
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 171 gcagggaacctggaatgggctgtgtgttctgcaagaaattggagccggtggccacggcca 230
Query: 193 aggaggatgctggcctggaaggggacttcagaagctacggggcagcagaccactatgggc 252
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 231 aggaggatgctggcctggaaggggacttcagaagctacggggcagcagaccactatgggc 290
Query: 253 ctgaccccactaaggcccggcctgcatcctcatttgcccacatccccaactacagcaact 312
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 291 ctgaccccactaaggcccggcctgcatcctcatttgcccacatccccaactacagcaact 350
Query: 313 tctcctctcaggccatcaaccctggcttccttgatagtggcaccatcaggggtgtgtcag 372
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 351 tctcctctcaggccatcaaccctggcttccttgatagtggcaccatcaggggtgtgtcag 410
Query: 373 ggattggggtgaccctgttcattgccctgtatgactatgaggctcgaactgaggatgacc 432
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 411 ggattggggtgaccctgttcattgccctgtatgactatgaggctcgaactgaggatgacc 470
Query: 433 tcaccttcaccaagggcgagaagttccacatcctgaacaatactgaaggtgactggtggg 492
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 471 tcaccttcaccaagggcgagaagttccacatcctgaacaatactgaaggtgactggtggg 530
Query: 493 aggctcggtctctcagctccggaaaaactggctgcattcccagcaactacgtggcccctg 552
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 531 aggctcggtctctcagctccggaaaaactggctgcattcccagcaactacgtggcccctg 590
Query: 553 ttgactcaatccaagctgaagagtggtactttggaaagattgggagaaaggatgcagaga 612
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 591 ttgactcaatccaagctgaagagtggtactttggaaagattgggagaaaggatgcagaga 650
Query: 613 ggcagctgctttcaccaggcaacccccagggggcctttctcattcgggaaagcgagacca 672
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 651 ggcagctgctttcaccaggcaacccccagggggcctttctcattcgggaaagcgagacca 710
Query: 673 ccaaaggtgcctactccctgtccatccgggactgggatcagaccagaggcgatcatgtga 732
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 711 ccaaaggtgcctactccctgtccatccgggactgggatcagaccagaggcgatcatgtga 770
Query: 733 agcattacaagatccgcaaactggacatgggcggctactacatcaccacacgggttcagt 792
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 771 agcattacaagatccgcaaactggacatgggcggctactacatcaccacacgggttcagt 830
Query: 793 tcaactcggtgcaggagctggtgcagcactacatggaggtgaatgacgggctgtgcaacc 852
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 831 tcaactcggtgcaggagctggtgcagcactacatggaggtgaatgacgggctgtgcaacc 890
Query: 853 tgctcatcgcgccctgcaccatcatgaagccgcagacgctgggcctggccaaggacgcct 912
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 891 tgctcatcgcgccctgcaccatcatgaagccgcagacgctgggcctggccaaggacgcct 950
Query: 913 gggagatcagccgcagctccatcacgctggagcgccggctgggcaccggctgcttcgggg 972
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 951 gggagatcagccgcagctccatcacgctggagcgccggctgggcaccggctgcttcgggg 1010
Query: 973 atgtgtggctgggcacgtggaacggcagcactaaggtggcggtgaagacgctgaagccgg 1032
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1011 atgtgtggctgggcacgtggaacggcagcactaaggtggcggtgaagacgctgaagccgg 1070
Query: 1033 gcaccatgtccccgaaggccttcctggaggaggcgcaggtcatgaagctgctgcggcacg 1092
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1071 gcaccatgtccccgaaggccttcctggaggaggcgcaggtcatgaagctgctgcggcacg 1130
Query: 1093 acaagctggtgcagctgtacgccgtggtgtcggaggagcccatctacatcgtgaccgagt 1152
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1131 acaagctggtgcagctgtacgccgtggtgtcggaggagcccatctacatcgtgaccgagt 1190
Query: 1153 tcatgtgtcacggcagcttgctggattttctcaagaacccagagggccaggatttgaggc 1212
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1191 tcatgtgtcacggcagcttgctggattttctcaagaacccagagggccaggatttgaggc 1250
Query: 1213 tgccccaattggtggacatggcagcccaggtagctgagggcatggcctacatggaacgca 1272
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1251 tgccccaattggtggacatggcagcccaggtagctgagggcatggcctacatggaacgca 1310
Query: 1273 tgaactacattcaccgcgacctgagggcagccaacatcctggttggggagcggctggcgt 1332
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1311 tgaactacattcaccgcgacctgagggcagccaacatcctggttggggagcggctggcgt 1370
Query: 1333 gcaagatcgcagactttggcttggcgcgtctcatcaaggacgatgagtacaacccctgcc 1392
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1371 gcaagatcgcagactttggcttggcgcgtctcatcaaggacgatgagtacaacccctgcc 1430
Query: 1393 aaggttccaagttccccatcaagtggacagccccagaagctgccctctttggcagattca 1452
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1431 aaggttccaagttccccatcaagtggacagccccagaagctgccctctttggcagattca 1490
Query: 1453 ccatcaagtcagacgtgtggtcctttgggatcctgctcactgagctca 1500
||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1491 ccatcaagtcagacgtgtggtcctttgggatcctgctcactgagctca 1538
>ENST00000217351 Gene:ENSG00000101371 Clone:AL133293
Contig:AL133293.28.1.68662 Chr:20 Basepair:35741025
Status:known
Length = 3668
Score = 147 bits (74), Expect = 4e-34
Identities = 206/250 (82%)
Strand = Plus / Plus
Query: 1251 ggcatggcctacatggaacgcatgaactacattcaccgcgacctgagggcagccaacatc 1310
|||||||| ||| |||| || ||||||||| | ||||| ||||| | ||||||||||||
Sbjct: 1144 ggcatggcgtacgtggagcggatgaactacgtccaccgggaccttcgtgcagccaacatc 1203
Query: 1311 ctggttggggagcggctggcgtgcaagatcgcagactttggcttggcgcgtctcatcaag 1370
||||| || ||| |||| |||||| | || |||||||| |||| || ||||| |
Sbjct: 1204 ctggtgggagagaacctggtgtgcaaagtggcggactttgggctggctcggctcattgaa 1263
Query: 1371 gacgatgagtacaacccctgccaaggttccaagttccccatcaagtggacagccccagaa 1430
||| ||||||||| | | |||||| |||| ||||||||||||||||| || ||||||
Sbjct: 1264 gacaatgagtacacggcgcggcaaggtgccaaattccccatcaagtggacggctccagaa 1323
Query: 1431 gctgccctctttggcagattcaccatcaagtcagacgtgtggtcctttgggatcctgctc 1490
|||||||||| |||| | |||||||||||||| |||||||||||||| |||||||||||
Sbjct: 1324 gctgccctctatggccgcttcaccatcaagtcggacgtgtggtccttcgggatcctgctg 1383
Query: 1491 actgagctca 1500
||||||||||
Sbjct: 1384 actgagctca 1393
Score = 111 bits (56), Expect = 2e-23
Identities = 185/228 (81%)
Strand = Plus / Plus
Query: 960 ggctgcttcggggatgtgtggctgggcacgtggaacggcagcactaaggtggcggtgaag 1019
|||||||| || || |||||| |||| || |||||||| | ||| | |||||| | ||
Sbjct: 853 ggctgctttggcgaggtgtggatggggacctggaacggtaccaccagggtggccatcaaa 912
Query: 1020 acgctgaagccgggcaccatgtccccgaaggccttcctggaggaggcgcaggtcatgaag 1079
|| |||||||| ||||| ||||| || ||||||||||| ||||||| ||||||||||||
Sbjct: 913 accctgaagcctggcacgatgtctccagaggccttcctgcaggaggcccaggtcatgaag 972
Query: 1080 ctgctgcggcacgacaagctggtgcagctgtacgccgtggtgtcggaggagcccatctac 1139
|||| |||| || |||||||||||| |||| || ||||| || ||||||||||| |||
Sbjct: 973 aagctgaggcatgagaagctggtgcagttgtatgctgtggtttcagaggagcccatttac 1032
Query: 1140 atcgtgaccgagttcatgtgtcacggcagcttgctggattttctcaag 1187
||||| || |||| |||| | | || || |||||||| |||||||||
Sbjct: 1033 atcgtcacggagtacatgagcaaggggagtttgctggactttctcaag 1080
Score = 61.9 bits (31), Expect = 2e-08
Identities = 46/51 (90%)
Strand = Plus / Plus
Query: 729 gtgaagcattacaagatccgcaaactggacatgggcggctactacatcacc 779
|||||||| |||||||||||||| ||||||| ||||||| ||||||||||
Sbjct: 622 gtgaagcactacaagatccgcaagctggacagcggcggcttctacatcacc 672
Score = 60.0 bits (30), Expect = 7e-08
Identities = 39/42 (92%)
Strand = Plus / Plus
Query: 879 aagccgcagacgctgggcctggccaaggacgcctgggagatc 920
||||||||||| | ||||||||||||||| ||||||||||||
Sbjct: 772 aagccgcagactcagggcctggccaaggatgcctgggagatc 813
Score = 46.1 bits (23), Expect = 0.001
Identities = 59/71 (83%)
Strand = Plus / Plus
Query: 522 ggctgcattcccagcaactacgtggcccctgttgactcaatccaagctgaagagtggtac 581
|||| ||| ||||||||||||||||| || ||||| ||||| ||||| ||||||||
Sbjct: 415 ggctacatccccagcaactacgtggcgccctccgactccatccaggctgaggagtggtat 474
Query: 582 tttggaaagat 592
||||| |||||
Sbjct: 475 tttggcaagat 485
Score = 40.1 bits (20), Expect = 0.067
Identities = 26/28 (92%)
Strand = Plus / Plus
Query: 660 gaaagcgagaccaccaaaggtgcctact 687
||||| |||||||| |||||||||||||
Sbjct: 553 gaaagtgagaccacgaaaggtgcctact 580
>ENST00000229471 Gene:ENSG00000010810 Clone:AL158035
Contig:AL158035.14.1.218548 Chr:6 Basepair:111817882
Status:known
Length = 2328
Score = 95.6 bits (48), Expect = 1e-18
Identities = 87/100 (87%)
Strand = Plus / Plus
Query: 1053 ttcctggaggaggcgcaggtcatgaagctgctgcggcacgacaagctggtgcagctgtac 1112
||||| ||||| |||||| |||||||| |||| ||||||||||||||| ||||| ||
Sbjct: 1271 ttccttgaggaagcgcagatcatgaagaagctgaagcacgacaagctggtccagctctat 1330
Query: 1113 gccgtggtgtcggaggagcccatctacatcgtgaccgagt 1152
|| |||||||| |||||||||||||||||||| |||||||
Sbjct: 1331 gcagtggtgtctgaggagcccatctacatcgtcaccgagt 1370
Score = 69.9 bits (35), Expect = 7e-11
Identities = 89/107 (83%)
Strand = Plus / Plus
Query: 1392 caaggttccaagttccccatcaagtggacagccccagaagctgccctctttggcagattc 1451
|||||| | |||||||||||||||||||| ||||| || || ||||| | || || |||
Sbjct: 1610 caaggtgcaaagttccccatcaagtggacggcccccgaggcagccctgtacgggaggttc 1669
Query: 1452 accatcaagtcagacgtgtggtcctttgggatcctgctcactgagct 1498
|| |||||||| ||||||||||| ||||| ||| | ||||| |||||
Sbjct: 1670 acaatcaagtctgacgtgtggtcttttggaatcttactcacagagct 1716
Score = 69.9 bits (35), Expect = 7e-11
Identities = 56/63 (88%)
Strand = Plus / Plus
Query: 527 cattcccagcaactacgtggcccctgttgactcaatccaagctgaagagtggtactttgg 586
|||||||||||| || ||||| || |||||||| ||||| || |||||||||||||||||
Sbjct: 736 cattcccagcaattatgtggctccagttgactctatccaggcagaagagtggtactttgg 795
Query: 587 aaa 589
|||
Sbjct: 796 aaa 798
Score = 42.1 bits (21), Expect = 0.017
Identities = 45/53 (84%)
Strand = Plus / Plus
Query: 1224 gtggacatggcagcccaggtagctgagggcatggcctacatggaacgcatgaa 1276
|||||||||||||| ||||| |||| || ||||| ||||| || ||||||||
Sbjct: 1442 gtggacatggcagcacaggtggctgcaggaatggcttacatcgagcgcatgaa 1494
>ENST00000229470 Gene:ENSG00000010810 Clone:Z97989
Contig:Z97989.1.1.155937 Chr:6 Basepair:111817882
Status:known
Length = 1695
Score = 95.6 bits (48), Expect = 1e-18
Identities = 87/100 (87%)
Strand = Plus / Plus
Query: 1053 ttcctggaggaggcgcaggtcatgaagctgctgcggcacgacaagctggtgcagctgtac 1112
||||| ||||| |||||| |||||||| |||| ||||||||||||||| ||||| ||
Sbjct: 1012 ttccttgaggaagcgcagatcatgaagaagctgaagcacgacaagctggtccagctctat 1071
Query: 1113 gccgtggtgtcggaggagcccatctacatcgtgaccgagt 1152
|| |||||||| |||||||||||||||||||| |||||||
Sbjct: 1072 gcagtggtgtctgaggagcccatctacatcgtcaccgagt 1111
Score = 69.9 bits (35), Expect = 7e-11
Identities = 89/107 (83%)
Strand = Plus / Plus
Query: 1392 caaggttccaagttccccatcaagtggacagccccagaagctgccctctttggcagattc 1451
|||||| | |||||||||||||||||||| ||||| || || ||||| | || || |||
Sbjct: 1351 caaggtgcaaagttccccatcaagtggacggcccccgaggcagccctgtacgggaggttc 1410
Query: 1452 accatcaagtcagacgtgtggtcctttgggatcctgctcactgagct 1498
|| |||||||| ||||||||||| ||||| ||| | ||||| |||||
Sbjct: 1411 acaatcaagtctgacgtgtggtcttttggaatcttactcacagagct 1457
Score = 42.1 bits (21), Expect = 0.017
Identities = 45/53 (84%)
Strand = Plus / Plus
Query: 1224 gtggacatggcagcccaggtagctgagggcatggcctacatggaacgcatgaa 1276
|||||||||||||| ||||| |||| || ||||| ||||| || ||||||||
Sbjct: 1183 gtggacatggcagcacaggtggctgcaggaatggcttacatcgagcgcatgaa 1235
>ENST00000012102 Gene:ENSG00000010810 Clone:Z97989
Contig:Z97989.1.1.155937 Chr:6 Basepair:111817882
Status:known
Length = 1602
Score = 95.6 bits (48), Expect = 1e-18
Identities = 87/100 (87%)
Strand = Plus / Plus
Query: 1053 ttcctggaggaggcgcaggtcatgaagctgctgcggcacgacaagctggtgcagctgtac 1112
||||| ||||| |||||| |||||||| |||| ||||||||||||||| ||||| ||
Sbjct: 922 ttccttgaggaagcgcagatcatgaagaagctgaagcacgacaagctggtccagctctat 981
Query: 1113 gccgtggtgtcggaggagcccatctacatcgtgaccgagt 1152
|| |||||||| |||||||||||||||||||| |||||||
Sbjct: 982 gcagtggtgtctgaggagcccatctacatcgtcaccgagt 1021
Score = 69.9 bits (35), Expect = 7e-11
Identities = 89/107 (83%)
Strand = Plus / Plus
Query: 1392 caaggttccaagttccccatcaagtggacagccccagaagctgccctctttggcagattc 1451
|||||| | |||||||||||||||||||| ||||| || || ||||| | || || |||
Sbjct: 1261 caaggtgcaaagttccccatcaagtggacggcccccgaggcagccctgtacgggaggttc 1320
Query: 1452 accatcaagtcagacgtgtggtcctttgggatcctgctcactgagct 1498
|| |||||||| ||||||||||| ||||| ||| | ||||| |||||
Sbjct: 1321 acaatcaagtctgacgtgtggtcttttggaatcttactcacagagct 1367
Score = 69.9 bits (35), Expect = 7e-11
Identities = 56/63 (88%)
Strand = Plus / Plus
Query: 527 cattcccagcaactacgtggcccctgttgactcaatccaagctgaagagtggtactttgg 586
|||||||||||| || ||||| || |||||||| ||||| || |||||||||||||||||
Sbjct: 396 cattcccagcaattatgtggctccagttgactctatccaggcagaagagtggtactttgg 455
Query: 587 aaa 589
|||
Sbjct: 456 aaa 458
Score = 42.1 bits (21), Expect = 0.017
Identities = 45/53 (84%)
Strand = Plus / Plus
Query: 1224 gtggacatggcagcccaggtagctgagggcatggcctacatggaacgcatgaa 1276
|||||||||||||| ||||| |||| || ||||| ||||| || ||||||||
Sbjct: 1093 gtggacatggcagcacaggtggctgcaggaatggcttacatcgagcgcatgaa 1145
>ENST00000262651 Gene:ENSG00000101336 Clone:AL353092
Contig:AL353092.6.1.25010 Chr:20 Basepair:30428114
Status:known
Length = 2089
Score = 85.7 bits (43), Expect = 1e-15
Identities = 79/91 (86%)
Strand = Plus / Plus
Query: 1399 ccaagttccccatcaagtggacagccccagaagctgccctctttggcagattcaccatca 1458
||||||||||||||||||||||||| || ||||| | ||||||| ||||||||||
Sbjct: 1421 ccaagttccccatcaagtggacagctcctgaagccatcaactttggctccttcaccatca 1480
Query: 1459 agtcagacgtgtggtcctttgggatcctgct 1489
|||||||||| ||||||||||| ||||||||
Sbjct: 1481 agtcagacgtctggtcctttggtatcctgct 1511
Score = 40.1 bits (20), Expect = 0.067
Identities = 29/32 (90%)
Strand = Plus / Plus
Query: 1126 aggagcccatctacatcgtgaccgagttcatg 1157
||||||||||||||||| | || |||||||||
Sbjct: 1148 aggagcccatctacatcatcacggagttcatg 1179
Database: Homo_sapiens.cdna.fa
Posted date: Dec 5, 2002 2:33 PM
Number of letters in database: 54,878,749
Number of sequences in database: 27,628
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 5,768,408
Number of Sequences: 27628
Number of extensions: 5768408
Number of successful extensions: 1106
Number of sequences better than 1.0e-01: 15
length of query: 1500
length of database: 54,878,749
effective HSP length: 18
effective length of query: 1482
effective length of database: 54,381,445
effective search space: 80593301490
effective search space used: 80593301490
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 20 (40.1 bits)
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