Hi,
Here is a truncated example of the blast output that causes the biojava
blast parser to print out error messages.
Thanks,
Emily
BLASTN 2.2.13 [Nov-27-2005]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
RID: 1142225124-9513-115032994966.BLASTQ1
Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
3,777,692 sequences; 16,788,289,139 total letters
Query= gi|27477090|ref|NM_000589.2| Homo sapiens interleukin 4 (IL4),
transcript
variant 1, mRNA
Length=921
Score
E
Sequences producing significant alignments: (Bits)
Value
gi|27477090|ref|NM_000589.2| Homo sapiens interleukin 4 (IL4), t 1649
0.0
gi|45708995|gb|BC067514.1| Homo sapiens interleukin 4, transc... 1045
0.0
gi|186334|gb|M13982.1|HUMIL4 Human interleukin 4 (IL-4) mRNA, co 1039
0.0
gi|45709847|gb|BC067515.1| Homo sapiens interleukin 4, transc... 1037
0.0
gi|47123366|gb|BC070123.1| Homo sapiens interleukin 4, transc... 1023
0.0
gi|42490870|gb|BC066277.1| Homo sapiens interleukin 4, transc... 1023
0.0
gi|42490899|gb|BC066278.1| Homo sapiens cDNA clone IMAGE:6971781 1021
0.0
gi|27477091|ref|NM_172348.1| Homo sapiens interleukin 4 (IL4), t 1003
0.0
gi|2811101|gb|AC004039.1| Homo sapiens chromosome 5, P1 clone... 1001
0.0
gi|14600279|gb|AF395008.1|AF395008 Homo sapiens interleukin 4 (I 1001
0.0
gi|1930572|gb|L81582.1|HSL81582 Homo sapiens (subclone 9_c5 f... 1001
0.0
gi|33831|emb|X06750.1|HSIL45 Human interleukin 4 gene 5'-region 1001
0.0
gi|186336|gb|M23442.1|HUMIL4A Human interleukin 4 (IL-4) gene, c 1001
0.0
gi|39980474|gb|AY480012.1| Pan troglodytes interleukin 13 (IL... 977
0.0
gi|37703741|gb|AY339646.1| Gorilla gorilla interleukin 4 (IL4... 977
0.0
gi|37703740|gb|AY339645.1| Pan paniscus interleukin 4 (IL4) g... 977
0.0
gi|37703739|gb|AY339644.1| Pan troglodytes interleukin 4 (IL4... 977
0.0
gi|62990254|gb|AC157216.2| Pan troglodytes BAC clone CH251-66... 977
0.0
gi|37703742|gb|AY339647.1| Pongo pygmaeus interleukin 4 (IL4)... 969
0.0
gi|61358435|gb|AY888625.1| Synthetic construct Homo sapiens c... 916
0.0
gi|61368530|gb|AY891269.1| Synthetic construct Homo sapiens c... 912
0.0
gi|60828588|gb|AY893811.1| Synthetic construct Homo sapiens c... 912
0.0
gi|60816922|gb|AY893365.1| Synthetic construct Homo sapiens c... 912
0.0
gi|58743320|ref|NM_001011714.1| Pan troglodytes interleukin 4 (I 908
0.0
gi|22858883|gb|AY130260.1| Pan troglodytes interleukin-4 (IL-4) 908
0.0
gi|37703743|gb|AY339648.1| Papio papio interleukin 4 (IL4) ge... 904
0.0
gi|1841299|dbj|AB000515.1| Macaca fascicularis mRNA for IL-4 pre 797
0.0
gi|514383|gb|L26027.1|MACIN4A Macaca mulatta interleukin 4 mRNA, 797
0.0
gi|644793|gb|U19838.1|CTU19838 Cercocebus torquatus interleukin- 789
0.0
gi|29569760|gb|AY234221.1| Papio anubis interleukin-4 precursor 779
0.0
gi|74136370|ref|NM_001032904.1| Macaca mulatta interleukin-4 (LO 773
0.0
gi|37014164|gb|AY376144.1| Macaca mulatta interleukin-4 mRNA, co 773
0.0
gi|20452370|gb|AF465829.1| Homo sapiens interleukin 4-like (IL4) 684
0.0
gi|40804376|gb|AY486435.1| Cercocebus torquatus atys interleu... 642
0.0
gi|40804375|gb|AY486434.1| Macaca mulatta interleukin 4 (IL-4) g 634
1e-178
gi|555892|gb|U14131.1|BTIL4S1 Bos taurus interleukin 4 (IL4) gen 561
1e-156
gi|673418|emb|X81851.1|HSIL4SV H. sapiens IL-4 gene splice varia 559
6e-156
gi|58736974|dbj|AB102862.1| Homo sapiens IL4 mRNA for interle... 559
6e-156
gi|22858887|gb|AY130262.1| Macaca fascicularis interleukin-4 ... 559
6e-156
gi|19918909|gb|AY083267.1| Macaca mulatta IL-4 gene, promoter re 553
3e-154
gi|58743332|ref|NM_001008993.1| Pan troglodytes interleukin 4 (I 551
1e-153
gi|22858885|gb|AY130261.1| Pan troglodytes interleukin-4 delt... 551
1e-153
gi|2905623|gb|AF043336.1|AF043336 Homo sapiens interleukin 4 del 551
1e-153
gi|19918910|gb|AY083268.1| Macaca radiata IL-4 gene, promoter re 545
8e-152
gi|4102679|gb|AF014509.1| Aotus nancymaae interleukin-4 (IL-4) m 545
8e-152
gi|6648935|gb|AF097321.1| Aotus lemurinus interleukin-4 (IL-4) m 545
8e-152
gi|6648933|gb|AF097320.1| Aotus nigriceps interleukin-4 (IL-4) m 545
8e-152
gi|4102669|gb|AF014504.1| Aotus vociferans interleukin-4 (IL-4) 537
2e-149
gi|25991896|gb|AF457197.1| Macaca mulatta interleukin 4 mRNA, pa 502
1e-138
gi|8575472|gb|AF235038.1|AF235038 Homo sapiens interleukin 4 (IL 486
7e-134
gi|18654097|gb|L81736.1|HUM11DC9S Homo sapiens (subclone 5_f7 fr 355
2e-94
gi|18654096|gb|L81735.1|HUM11DC92S Homo sapiens (subclone 8_e7 f 355
2e-94
gi|1930575|gb|L81579.1|HSL81579 Homo sapiens (subclone 5_f7 f... 355
2e-94
gi|1930574|gb|L81580.1|HSL81580 Homo sapiens (subclone 8_e7 f... 355
2e-94
gi|34419654|gb|AC107611.6| Rattus norvegicus 10 BAC CH230-195... 278
3e-71
gi|56481|emb|X53087.1|RNIL4E12 R.norvegicus gene for interleukin 270
7e-69
gi|545218|gb|S69238.1| IL4 {promoter} [mice, BALB/c, Genomic, 82 222
2e-54
gi|52678|emb|X05064.1|MMIL4G12 Mouse interleukin 4 gene exons 1 222
2e-54
gi|57157560|dbj|AB174764.1| Mus musculus molossinus IL-4 gene... 220
6e-54
gi|3687208|gb|AC005742.1| Mus musculus chromosome 11, BAC clo... 214
4e-52
gi|11038606|gb|AC084392.1| Mus musculus BAC clone GS1-182G5 from 214
4e-52
gi|545217|gb|S69237.1| IL4 {promoter} [mice, C57BL/6, Genomic, 8 214
4e-52
gi|21211994|emb|AL645741.15| Mouse DNA sequence from clone RP... 214
4e-52
gi|27960676|gb|AF463769.1| Mus musculus strain C57BL/6J cytok... 214
4e-52
gi|1930579|gb|L81578.1|HSL81578 Homo sapiens (subclone 2_b2 f... 204
4e-49
gi|4996849|dbj|AB020732.1| Tursiops truncatus mRNA for interleuk 192
1e-45
gi|163212|gb|M84745.1|BOVIL4XX Bovine interleukin 4 (IL4) gene, 180
5e-42
gi|20530678|gb|AF493991.1| Sus scrofa interleukin-4 precursor (I 141
5e-30
gi|1997|emb|X68330.1|SSILK4 S.scrofa mRNA for interleukin-4 141
5e-30
gi|55742621|ref|NM_214123.1| Sus scrofa interleukin 4 (IL4), mRN 141
5e-30
gi|1730275|gb|U34273.1|CHU34273 Capra hircus interleukin-4 mRNA, 141
5e-30
gi|294220|gb|L12991.1|PIGIL4A Pig interleukin 4 mRNA, complete c 133
1e-27
gi|29603606|dbj|AB107648.1| Lama glama IL-4 mRNA for interleukin 131
4e-27
gi|32186777|gb|AY294020.1| Sus scrofa interleukin 4 mRNA, comple 125
3e-25
gi|57527819|ref|NM_001009313.2| Ovis aries interleukin 4 (IL4), 125
3e-25
gi|165950|gb|M96845.1|SHPIL4A Sheep interleukin 4 mRNA, complete 125
3e-25
gi|84794457|dbj|AB246673.1| Camelus bactrianus IL-4 mRNA for int 123
1e-24
gi|163891|gb|L07081.1|CEUINTERLU Cervus elaphus (clone SH3) inte 119
2e-23
gi|164233|gb|L06010.1|HRSIL4X Horse interleukin 4 mRNA, partial 97.6
6e-17
gi|50096517|gb|AY648947.1| Capra hircus interleukin-4 mRNA, comp 87.7
6e-14
gi|31416286|gb|AY293620.1| Bubalus bubalis interleukin 4 (IL-4) 83.8
9e-13
gi|84875352|dbj|AB246356.1| Bubalus bubalis x Bubalus caraban... 83.8
9e-13
gi|84871721|dbj|AB246355.1| Bubalus bubalis IL-4 mRNA for interl 83.8
9e-13
gi|84871699|dbj|AB246275.1| Bubalus carabanensis IL-4 mRNA for i 83.8
9e-13
gi|31343261|ref|NM_173921.2| Bos taurus interleukin 4 (IL4), mRN 83.8
9e-13
gi|163210|gb|M77120.1|BOVIL4X Bovine interleukin 4 (IL4) mRNA, c 83.8
9e-13
gi|46310147|gb|AY575607.1| Ovis aries interleukin 4 (IL-4) mR... 81.8
4e-12
gi|46310145|gb|AY575606.1| Ovis aries interleukin 4 (IL-4) mR... 81.8
4e-12
gi|21217734|gb|AY096800.1| Ovis aries interleukin-4 precursor, m 81.8
4e-12
gi|2654199|gb|AF035404.1| Equus caballus interleukin-4 precur... 81.8
4e-12
gi|1277|emb|Z11897.1|OAIL4MRNA O.aries IL-4 mRNA for interleukin 81.8
4e-12
gi|5732983|gb|AF172168.1|AF172168 Ovis aries interleukin 4 mRNA, 81.8
4e-12
gi|10716183|gb|AF305617.1|AF305617 Equus caballus interleukin 4 81.8
4e-12
gi|60687486|gb|AY939910.1| Boselaphus tragocamelus interleukin-4 81.8
4e-12
gi|50978885|ref|NM_001003159.1| Canis familiaris interleukin 4 ( 75.8
2e-10
gi|7330263|gb|AF239917.1|AF239917 Canis familiaris interleukin-4 75.8
2e-10
gi|13346438|gb|AF346295.1|AF346295 Phocoena phocoena interleukin 75.8
2e-10
gi|6007792|gb|AF187322.1|AF187322 Canis familiaris interleukin-4 75.8
2e-10
gi|4185290|gb|AF083270.1|AF083270 Canis familiaris interleuki... 75.8
2e-10
gi|14029512|gb|AF333965.1| Marmota monax interleukin-4 mRNA, par 67.9
5e-08
ALIGNMENTS
gi|27477090|ref|NM_000589.2| Homo sapiens interleukin 4 (IL4), transcript
variant 1, mRNA
Length=921
Score = 1649 bits (832), Expect = 0.0
Identities = 832/832 (100%), Gaps = 0/832 (0%)
Strand=Plus/Plus
Query 1 TTCTATGCAAAGCAAAAAGCCAGCAGCAGCCCCAAGCTGATAAGATTAATCTAAAGAGCA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1 TTCTATGCAAAGCAAAAAGCCAGCAGCAGCCCCAAGCTGATAAGATTAATCTAAAGAGCA 60
Query 61 AATTATGGTGTAATTTCCTATGCTGAAACTTTGTAGTTAATTTTTTAAAAAGGTTTCATT
120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 61 AATTATGGTGTAATTTCCTATGCTGAAACTTTGTAGTTAATTTTTTAAAAAGGTTTCATT
120
Query 121 TTCCTATTGGTCTGATTTCACAGGAACATTTTACCTGTTTGTGAGGCATTTTTTCTCCTG
180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 121 TTCCTATTGGTCTGATTTCACAGGAACATTTTACCTGTTTGTGAGGCATTTTTTCTCCTG
180
Query 181 GAAGAGAGGTGCTGATTGGCCCCAAGTGACTGACAATCTGGTGTAACGAAAATTTCCAAT
240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 181 GAAGAGAGGTGCTGATTGGCCCCAAGTGACTGACAATCTGGTGTAACGAAAATTTCCAAT
240
Query 241 GTAAACTCATTTTCCCTCGGTTTCAGCAATTTTAAATCTATATATAGAGATATCTTTGTC
300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 241 GTAAACTCATTTTCCCTCGGTTTCAGCAATTTTAAATCTATATATAGAGATATCTTTGTC
300
Query 301 AGCATTGCATCGTTAGCTTCTCCTGATAAACTAATTGCCTCACATTGTCACTGCAAATCG
360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 301 AGCATTGCATCGTTAGCTTCTCCTGATAAACTAATTGCCTCACATTGTCACTGCAAATCG
360
Query 361 ACACCTATTAATGGGTCTCACCTCCCAACTGCTTCCCCCTCTGTTCTTCCTGCTAGCATG
420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 361 ACACCTATTAATGGGTCTCACCTCCCAACTGCTTCCCCCTCTGTTCTTCCTGCTAGCATG
420
Query 421 TGCCGGCAACTTTGTCCACGGACACAAGTGCGATATCACCTTACAGGAGATCATCAAAAC
480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 421 TGCCGGCAACTTTGTCCACGGACACAAGTGCGATATCACCTTACAGGAGATCATCAAAAC
480
Query 481 TTTGAACAGCCTCACAGAGCAGAAGACTCTGTGCACCGAGTTGACCGTAACAGACATCTT
540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 481 TTTGAACAGCCTCACAGAGCAGAAGACTCTGTGCACCGAGTTGACCGTAACAGACATCTT
540
Query 541 TGCTGCCTCCAAGAACACAACTGAGAAGGAAACCTTCTGCAGGGCTGCGACTGTGCTCCG
600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 541 TGCTGCCTCCAAGAACACAACTGAGAAGGAAACCTTCTGCAGGGCTGCGACTGTGCTCCG
600
Query 601 GCAGTTCTACAGCCACCATGAGAAGGACACTCGCTGCCTGGGTGCGACTGCACAGCAGTT
660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 601 GCAGTTCTACAGCCACCATGAGAAGGACACTCGCTGCCTGGGTGCGACTGCACAGCAGTT
660
Query 661 CCACAGGCACAAGCAGCTGATCCGATTCCTGAAACGGCTCGACAGGAACCTCTGGGGCCT
720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 661 CCACAGGCACAAGCAGCTGATCCGATTCCTGAAACGGCTCGACAGGAACCTCTGGGGCCT
720
Query 721 GGCGGGCTTGAATTCCTGTCCTGTGAAGGAAGCCAACCAGAGTACGTTGGAAAACTTCTT
780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 721 GGCGGGCTTGAATTCCTGTCCTGTGAAGGAAGCCAACCAGAGTACGTTGGAAAACTTCTT
780
Query 781 GGAAAGGCTAAAGACGATCATGAGAGAGAAATATTCAAAGTGTTCGAGCTGA 832
||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 781 GGAAAGGCTAAAGACGATCATGAGAGAGAAATATTCAAAGTGTTCGAGCTGA 832
gi|45708995|gb|BC067514.1| Homo sapiens interleukin 4, transcript variant
1, mRNA (cDNA
clone MGC:79403 IMAGE:6971780), complete cds
Length=528
Score = 1045 bits (527), Expect = 0.0
Identities = 527/527 (100%), Gaps = 0/527 (0%)
Strand=Plus/Plus
Query 306 TGCATCGTTAGCTTCTCCTGATAAACTAATTGCCTCACATTGTCACTGCAAATCGACACC
365
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1 TGCATCGTTAGCTTCTCCTGATAAACTAATTGCCTCACATTGTCACTGCAAATCGACACC 60
Query 366 TATTAATGGGTCTCACCTCCCAACTGCTTCCCCCTCTGTTCTTCCTGCTAGCATGTGCCG
425
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 61 TATTAATGGGTCTCACCTCCCAACTGCTTCCCCCTCTGTTCTTCCTGCTAGCATGTGCCG
120
Query 426 GCAACTTTGTCCACGGACACAAGTGCGATATCACCTTACAGGAGATCATCAAAACTTTGA
485
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 121 GCAACTTTGTCCACGGACACAAGTGCGATATCACCTTACAGGAGATCATCAAAACTTTGA
180
Query 486 ACAGCCTCACAGAGCAGAAGACTCTGTGCACCGAGTTGACCGTAACAGACATCTTTGCTG
545
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 181 ACAGCCTCACAGAGCAGAAGACTCTGTGCACCGAGTTGACCGTAACAGACATCTTTGCTG
240
Query 546 CCTCCAAGAACACAACTGAGAAGGAAACCTTCTGCAGGGCTGCGACTGTGCTCCGGCAGT
605
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 241 CCTCCAAGAACACAACTGAGAAGGAAACCTTCTGCAGGGCTGCGACTGTGCTCCGGCAGT
300
Query 606 TCTACAGCCACCATGAGAAGGACACTCGCTGCCTGGGTGCGACTGCACAGCAGTTCCACA
665
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 301 TCTACAGCCACCATGAGAAGGACACTCGCTGCCTGGGTGCGACTGCACAGCAGTTCCACA
360
Query 666 GGCACAAGCAGCTGATCCGATTCCTGAAACGGCTCGACAGGAACCTCTGGGGCCTGGCGG
725
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 361 GGCACAAGCAGCTGATCCGATTCCTGAAACGGCTCGACAGGAACCTCTGGGGCCTGGCGG
420
Query 726 GCTTGAATTCCTGTCCTGTGAAGGAAGCCAACCAGAGTACGTTGGAAAACTTCTTGGAAA
785
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 421 GCTTGAATTCCTGTCCTGTGAAGGAAGCCAACCAGAGTACGTTGGAAAACTTCTTGGAAA
480
Query 786 GGCTAAAGACGATCATGAGAGAGAAATATTCAAAGTGTTCGAGCTGA 832
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 481 GGCTAAAGACGATCATGAGAGAGAAATATTCAAAGTGTTCGAGCTGA 527
gi|186334|gb|M13982.1|HUMIL4 Human interleukin 4 (IL-4) mRNA, complete cds
Length=614
Score = 1039 bits (524), Expect = 0.0
Identities = 524/524 (100%), Gaps = 0/524 (0%)
Strand=Plus/Plus
Query 309 ATCGTTAGCTTCTCCTGATAAACTAATTGCCTCACATTGTCACTGCAAATCGACACCTAT
368
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 2 ATCGTTAGCTTCTCCTGATAAACTAATTGCCTCACATTGTCACTGCAAATCGACACCTAT 61
Query 369 TAATGGGTCTCACCTCCCAACTGCTTCCCCCTCTGTTCTTCCTGCTAGCATGTGCCGGCA
428
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 62 TAATGGGTCTCACCTCCCAACTGCTTCCCCCTCTGTTCTTCCTGCTAGCATGTGCCGGCA
121
Query 429 ACTTTGTCCACGGACACAAGTGCGATATCACCTTACAGGAGATCATCAAAACTTTGAACA
488
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 122 ACTTTGTCCACGGACACAAGTGCGATATCACCTTACAGGAGATCATCAAAACTTTGAACA
181
Query 489 GCCTCACAGAGCAGAAGACTCTGTGCACCGAGTTGACCGTAACAGACATCTTTGCTGCCT
548
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 182 GCCTCACAGAGCAGAAGACTCTGTGCACCGAGTTGACCGTAACAGACATCTTTGCTGCCT
241
Query 549 CCAAGAACACAACTGAGAAGGAAACCTTCTGCAGGGCTGCGACTGTGCTCCGGCAGTTCT
608
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 242 CCAAGAACACAACTGAGAAGGAAACCTTCTGCAGGGCTGCGACTGTGCTCCGGCAGTTCT
301
Query 609 ACAGCCACCATGAGAAGGACACTCGCTGCCTGGGTGCGACTGCACAGCAGTTCCACAGGC
668
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 302 ACAGCCACCATGAGAAGGACACTCGCTGCCTGGGTGCGACTGCACAGCAGTTCCACAGGC
361
Query 669 ACAAGCAGCTGATCCGATTCCTGAAACGGCTCGACAGGAACCTCTGGGGCCTGGCGGGCT
728
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 362 ACAAGCAGCTGATCCGATTCCTGAAACGGCTCGACAGGAACCTCTGGGGCCTGGCGGGCT
421
Query 729 TGAATTCCTGTCCTGTGAAGGAAGCCAACCAGAGTACGTTGGAAAACTTCTTGGAAAGGC
788
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 422 TGAATTCCTGTCCTGTGAAGGAAGCCAACCAGAGTACGTTGGAAAACTTCTTGGAAAGGC
481
Query 789 TAAAGACGATCATGAGAGAGAAATATTCAAAGTGTTCGAGCTGA 832
||||||||||||||||||||||||||||||||||||||||||||
Sbjct 482 TAAAGACGATCATGAGAGAGAAATATTCAAAGTGTTCGAGCTGA 525
From: [EMAIL PROTECTED]
To: "Emily Wong" <[EMAIL PROTECTED]>
CC: [email protected], [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Blast parser for ncbi blast version 2.2.13
Date: Tue, 14 Mar 2006 09:07:39 +0800
Possibly some variation in this output is causing the problem
Can you post some blast output that replicates this error?
Thanks
- Mark
"Emily Wong" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
03/13/2006 01:39 PM
To: [email protected]
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Blast parser for ncbi blast version
2.2.13
Hi,
Is there a parser that takes into account ncbi blast version 2.2.13(on
their
website)? I am trying to use the code here to parse :
http://www.biojava.org/docs/bj_in_anger/BlastParser.htm . If I set the
parser from strict to lazy I get these comments :
Exception in thread "main" java.lang.NullPointerException
at
org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:215)
at
org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:164)
at
org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311)
at
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274)
at
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)
at BlastParser.main(BlastParser.java:46)
Thanks,
Emily
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
