#!/usr/bin/perl use warnings; use strict; use Bio::SearchIO; use Bio::AlignIO; use strict; my $out = "C:/Documents and Settings/mydir/Desktop/current/bl2seq/13117_aln.out"; my $dir = 'C:/Documents and Settings/mydir/Desktop/current/bl2seq/'; my $in = new Bio::SearchIO(-format => 'blast', -file => $dir.'13117_2.out'); while( my $result = $in->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { if( $hsp->length('total') > 1000 ) { if ( $hsp->percent_identity >= 90 ) { if( $hsp->score ){ if( $hsp->gaps ){ if( $hsp->expect ){ print "Hit= ", $hit->name, " Length=", $hsp->length('total'), " Score=", $hsp->score,"\n"; print "Gaps=", $hsp->gaps, " Expect=", $hsp->expect, " Percent_id=", $hsp->percent_identity, "\n"; my $aln = $hsp->get_aln; my $alnIO = Bio::AlignIO->new(-format =>"clustalw", -file => $out); $alnIO->write_aln($aln); } } } } } } } } __DATA__ Query= 13117 Mus musculus genomic with Cassette inserted (10,084 letters) >13117/13117_fasta.Contig1 Length = 1453 Score = 2046 bits (1032), Expect = 0.0 Identities = 1088/1100 (98%), Gaps = 5/1100 (0%) Strand = Plus / Minus Query: 1001 taggaaccattttttttttttct-gtgtttccttca-tcctgtgactctgccaacc-aac 1057 ||||||||||||||||||||| | |||||||||||| |||||||||||| |||||| ||| Sbjct: 1113 taggaaccatttttttttttttttgtgtttccttcaatcctgtgactctaccaacccaac 1054 Query: 1058 tttctaatccctctacctgcaaactacaaactctggtctgccagcaggttatgaattgta 1117 |||||||||| ||||||||||||||||||||||||||||||||||||||||| |||| || Sbjct: 1053 tttctaatccttctacctgcaaactacaaactctggtctgccagcaggttataaatttta 994 Query: 1118 aagaaatttcattatgcttttgtctgcaaaatcccccagttctcagaaacaggg-ttaaa 1176 |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| Sbjct: 993 aagaaatttcattatgcttttgtctgcaaaatcccccagttctcagaaacaggggttaaa 934 Query: 1177 gccaatgtgtagagaagaatgaacaaaa-tgcagaaatgcagggaatcccagtgcctcat 1235 ||||||| |||||||||||||||||||| |||||||| |||||||||||||||||||||| Sbjct: 933 gccaatgggtagagaagaatgaacaaaaatgcagaaaagcagggaatcccagtgcctcat 874 Query: 1236 ggggtgggggtggggtgggagtgcagggtcagcagggaccatccagatgctgggacaccc 1295 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 873 ggggtgggggtggggtgggagtgcagggtcagcagggaccatccagatgctgggacaccc 814 Query: 1296 ctgtgaaatatcacaccctctctgccccgtgctgtcctggattcaggtcaaactggattt 1355 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 813 ctgtgaaatatcacaccctctctgccccgtgctgtcctggattcaggtcaaactggattt 754 Query: 1356 caatctgcataatttgtcccatttagaagggttgggagagggtgagaacaggagggtgaa 1415 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 753 caatctgcataatttgtcccatttagaagggttgggagagggtgagaacaggagggtgaa 694 Query: 1416 gactgaggaggggggatagatactccccccatcccaaaggcaggcatgaagtagtggcca 1475 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 693 gactgaggaggggggatagatactccccccatcccaaaggcaggcatgaagtagtggcca 634 Query: 1476 gaggaaaccagagtgaacaggctggagtgaaggctggtagctgctagagagaggaggtgg 1535 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 633 gaggaaaccagagtgaacaggctggagtgaaggctggtagctgctagagagaggaggtgg 574 Query: 1536 gaccgggaggagcagcaggcttgaaaagcacagggtaattgtcagcccagcactgtaggg 1595 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 573 gaccgggaggagcagcaggcttgaaaagcacagggtaattgtcagcccagcactgtaggg 514 Query: 1596 ggcaatttagtctacttacccagtggcaagaagtaaaaaaaaagtgggctgtgacttaaa 1655 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 513 ggcaatttagtctacttacccagtggcaagaagtaaaaaaaaagtgggctgtgacttaaa 454 Query: 1656 gatcttaagactcactagagagggaggggttagcctgggagtgggaggagggagtgcaga 1715 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 453 gatcttaagactcactagagagggaggggttagcctgggagtgggaggagggagtgcaga 394 Query: 1716 gtttaggaggagacagagactctggagggtgcaaggaagtgtctttagctgagctgggct 1775 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 393 gtttaggaggagacagagactctggagggtgcaaggaagtgtctttagctgagctgggct 334 Query: 1776 gggctgggacgggaaggtagactgaagctgcctgaactgctcatcccgctgggtctgagc 1835 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 333 gggctgggacgggaaggtagactgaagctgcctgaactgctcatcccgctgggtctgagc 274 Query: 1836 tcccagtggggcggttcgcatgcctggaaggactctaagcaccctcagacctcttactct 1895 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 273 tcccagtggggcggttcgcatgcctggaaggactctaagcaccctcagacctcttactct 214 Query: 1896 gaggttcaagccaatccttcagggtgcttgctgagttggtgacccatctctggaactggt 1955 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 213 gaggttcaagccaatccttcagggtgcttgctgagttggtgacccatctctggaactggt 154 Query: 1956 gtccctgggactcactgcccagcttcacttcattcagcaccatgggtaccgatttaaatg 2015 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 153 gtccctgggactcactgcccagcttcacttcattcagcaccatgggtaccgatttaaatg 94 Query: 2016 atccagtggtcctgcagaggagagattgggagaatcccggtgtgacacagctgaacagac 2075 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 93 atccagtggtcctgcagaggagagattgggagaatcccggtgtgacacagctgaacagac 34 Query: 2076 tagccgcccaccctcccttt 2095 |||||||||||||||||||| Sbjct: 33 tagccgcccaccctcccttt 14 Score = 40.1 bits (20), Expect = 1e-005 Identities = 20/20 (100%) Strand = Plus / Minus Query: 7698 ggggtgggggtggggtggga 7717 |||||||||||||||||||| Sbjct: 873 ggggtgggggtggggtggga 854 Score = 28.2 bits (14), Expect = 0.046 Identities = 14/14 (100%) Strand = Plus / Minus Query: 8817 catttttttttttt 8830 |||||||||||||| Sbjct: 1106 catttttttttttt 1093 Score = 26.3 bits (13), Expect = 0.18 Identities = 13/13 (100%) Strand = Plus / Plus Query: 363 cccctccctctct 375 ||||||||||||| Sbjct: 425 cccctccctctct 437 Score = 26.3 bits (13), Expect = 0.18 Identities = 13/13 (100%) Strand = Plus / Minus Query: 7649 agggtgagaacag 7661 ||||||||||||| Sbjct: 715 agggtgagaacag 703 Score = 24.3 bits (12), Expect = 0.71 Identities = 12/12 (100%) Strand = Plus / Plus Query: 5507 cccccctcctca 5518 |||||||||||| Sbjct: 679 cccccctcctca 690 Score = 24.3 bits (12), Expect = 0.71 Identities = 12/12 (100%) Strand = Plus / Minus Query: 8819 tttttttttttt 8830 |||||||||||| Sbjct: 1101 tttttttttttt 1090 Score = 24.3 bits (12), Expect = 0.71 Identities = 12/12 (100%) Strand = Plus / Minus Query: 8819 tttttttttttt 8830 |||||||||||| Sbjct: 1102 tttttttttttt 1091 Score = 24.3 bits (12), Expect = 0.71 Identities = 12/12 (100%) Strand = Plus / Minus Query: 8819 tttttttttttt 8830 |||||||||||| Sbjct: 1103 tttttttttttt 1092 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Minus Query: 598 tcctgcagagg 608 ||||||||||| Sbjct: 84 tcctgcagagg 74 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Minus Query: 4644 gcctgaactgc 4654 ||||||||||| Sbjct: 304 gcctgaactgc 294 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Minus Query: 4040 ctgcctgaact 4050 ||||||||||| Sbjct: 306 ctgcctgaact 296 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Minus Query: 9957 ttagctgagct 9967 ||||||||||| Sbjct: 349 ttagctgagct 339 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Plus Query: 9036 ctgtctcctcc 9046 ||||||||||| Sbjct: 378 ctgtctcctcc 388 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Plus Query: 7830 tcctcccactc 7840 ||||||||||| Sbjct: 405 tcctcccactc 415 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Minus Query: 368 ccctctctgcc 378 ||||||||||| Sbjct: 798 ccctctctgcc 788 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Plus Query: 9047 cccaccccacc 9057 ||||||||||| Sbjct: 855 cccaccccacc 865 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Plus Query: 9045 cccccacccca 9055 ||||||||||| Sbjct: 864 cccccacccca 874 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Plus Query: 8608 tttctgagaac 8618 ||||||||||| Sbjct: 945 tttctgagaac 955 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Plus Query: 564 aaaaaaaaaat 574 ||||||||||| Sbjct: 1095 aaaaaaaaaat 1105 Score = 22.3 bits (11), Expect = 2.8 Identities = 11/11 (100%) Strand = Plus / Minus Query: 7639 tttgttaagaa 7649 ||||||||||| Sbjct: 1436 tttgttaagaa 1426 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 Sequences: 1 Number of Hits to DB: 562 Number of extensions: 37 Number of successful extensions: 37 Number of sequences better than 10.0: 1 Number of HSP's gapped: 24 Number of HSP's successfully gapped: 21 Length of query: 10084 Length of database: 1453 Length adjustment: 12 Effective length of query: 10072 Effective length of database: 1441 Effective search space: 14513752 Effective search space used: 14513752 X1: 11 (21.8 bits) X2: 15 (29.7 bits) X3: 50 (99.1 bits) S1: 11 (22.3 bits) S2: 11 (22.3 bits)