blast的结果
做出来了诶O(∩_∩)O哈哈~ 有点小开心(*^▽^*)
conda装的blast做不出来，还不知道是什么原因。重新在自己家里装的blast运行没问题。
建库部分：遇到了一些关于grep、sed、awk还有for循环的问题，再开一篇记录吧。还有fa的格式问题。然后就是，原来blast是可以多对多比对的，那就可以一次性做批量处理了~
#建库
/home/hmguang/biosoft/blast/blast/ncbi-blast-2.9.0+/bin/makeblastdb -in refdata.fasta -dbtype nucl
#比对
/home/hmguang/biosoft/blast_project/blast/ncbi-blast-2.9.0+/bin/blastn -query testseq -out result.txt -db refdata.fasta -evalue 1e-5
结果：
BLASTN 2.9.0+
Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.
Database: refdata.fasta
? 16 sequences; 411,130 total letters
Query= YW607_F06
Length=524
? Score E
Sequences producing significant alignments: ? (Bits) Value
NC_000017.11:4932277-4935023Homosapienschromosome17_GP1BA,GRCh38....? 350 8e-98
NC_000017.11:4932277-4935023Homosapienschromosome17_GP1BA_core,GR...? 350 8e-98
>NC_000017.11:4932277-4935023Homosapienschromosome17_GP1BA,GRCh38.p13PrimaryAssembly
Length=2747
Score = 350 bits (189),? Expect = 8e-98
Identities = 194/197 (98%), Gaps = 0/197 (0%)
Strand=Plus/Minus
Query? 1 TACAGCGAGTTCTCTTGGAGGAGAAGGGTGTCGAGATTCTCCAGCCCATTCAGGAGCCCA? 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 930? TACAGCGAGTTCTCTTGGAGGAGAAGGGTGTCGAGATTCTCCAGCCCATTCAGGAGCCCA? 871
Query? 61? GCGGGGAGCTCAGTCAAGTTGTTGTTAGCCAGACTGAGCTTCTCCAGCTTGGGTGTGGGC? 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 870? GCGGGGAGCTCAGTCAAGTTGTTGTTAGCCAGACTGAGCTTCTCCAGCTTGGGTGTGGGC? 811
Query? 121? GTCAGGAGCCCTGGGGGCAGGGTCTTCAGCTCATTGCCTTTCAGGTAGAGCTCTTGGAGT? 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 810? GTCAGGAGCCCTGGGGGCAGGGTCTTCAGCTCATTGCCTTTCAGGTAGAGCTCTTGGAGT? 751
Query? 181? TCGCMAGTACCACGCAG? 197
|||| |? |||||||||
Sbjct? 750? TCGCCAAGACCACGCAG? 734
>NC_000017.11:4932277-4935023Homosapienschromosome17_GP1BA_core,GRCh38.p13PrimaryAssembly
Length=357
Score = 350 bits (189),? Expect = 8e-98
Identities = 194/197 (98%), Gaps = 0/197 (0%)
Strand=Plus/Minus
Query? 1 TACAGCGAGTTCTCTTGGAGGAGAAGGGTGTCGAGATTCTCCAGCCCATTCAGGAGCCCA? 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 295? TACAGCGAGTTCTCTTGGAGGAGAAGGGTGTCGAGATTCTCCAGCCCATTCAGGAGCCCA? 236
Query? 61? GCGGGGAGCTCAGTCAAGTTGTTGTTAGCCAGACTGAGCTTCTCCAGCTTGGGTGTGGGC? 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 235? GCGGGGAGCTCAGTCAAGTTGTTGTTAGCCAGACTGAGCTTCTCCAGCTTGGGTGTGGGC? 176
Query? 121? GTCAGGAGCCCTGGGGGCAGGGTCTTCAGCTCATTGCCTTTCAGGTAGAGCTCTTGGAGT? 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 175? GTCAGGAGCCCTGGGGGCAGGGTCTTCAGCTCATTGCCTTTCAGGTAGAGCTCTTGGAGT? 116
Query? 181? TCGCMAGTACCACGCAG? 197
|||| |? |||||||||
Sbjct? 115? TCGCCAAGACCACGCAG? 99
Lambda ? K H
1.37 0.632 1.16
Gapped
Lambda ? K H
1.28 0.460 0.850
Effective search space used: 207467130
Query= YW614_E07
Length=284
? Score E
Sequences producing significant alignments: ? (Bits) Value
NC_000005.10:52989326-53094779Homosapienschromosome5_ITGA2,GRCh38...? 291 3e-80
NC_000005.10:52989326-53094779Homosapienschromosome5_ITGA2_4core,...? 291 3e-80
>NC_000005.10:52989326-53094779Homosapienschromosome5_ITGA2,GRCh38.p13PrimaryAssembly
Length=105454
Score = 291 bits (157),? Expect = 3e-80
Identities = 161/164 (98%), Gaps = 0/164 (0%)
Strand=Plus/Plus
Query? 1 ? TTGTCAGCAACCAAAACAAAARGTTAACATTTTCAGTAACGCTGAAAAATAAAAGGGAAA? 60
? ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct? 83807? TTGTCAGCAACCAAAACAAAAGGTTAACATTTTCAGTAACGCTGAAAAATAAAAGGGAAA? 83866
Query? 61 GTGCATACAACACTGGAATTGTTGTTGATTTTTCAGAAAACTTGTTTTTTGCATCATTCT? 120
? ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 83867? GTGCATACAACACTGGAATTGTTGTTGATTTTTCAGAAAACTTGTTTTTTGCATCATTCT? 83926
Query? 121 CCCTGCCGGTATGTGATGAGACCCTGTACTTAYGTCCACCATGC? 164
? ||||||||||||||||||||||||||||||||? ||||||||||
Sbjct? 83927? CCCTGCCGGTATGTGATGAGACCCTGTACTTACTTCCACCATGC? 83970
>NC_000005.10:52989326-53094779Homosapienschromosome5_ITGA2_4core,GRCh38.p13PrimaryAssembly
Length=1671
Score = 291 bits (157),? Expect = 3e-80
Identities = 161/164 (98%), Gaps = 0/164 (0%)
Strand=Plus/Plus
Query? 1 TTGTCAGCAACCAAAACAAAARGTTAACATTTTCAGTAACGCTGAAAAATAAAAGGGAAA? 60
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct? 1022? TTGTCAGCAACCAAAACAAAAGGTTAACATTTTCAGTAACGCTGAAAAATAAAAGGGAAA? 1081
Query? 61 GTGCATACAACACTGGAATTGTTGTTGATTTTTCAGAAAACTTGTTTTTTGCATCATTCT? 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 1082? GTGCATACAACACTGGAATTGTTGTTGATTTTTCAGAAAACTTGTTTTTTGCATCATTCT? 1141
Query? 121? CCCTGCCGGTATGTGATGAGACCCTGTACTTAYGTCCACCATGC? 164
||||||||||||||||||||||||||||||||? ||||||||||
Sbjct? 1142? CCCTGCCGGTATGTGATGAGACCCTGTACTTACTTCCACCATGC? 1185
Lambda ? K H
1.42 0.646 1.21
Gapped
Lambda ? K H
1.28 0.460 0.850
Effective search space used: 109283972
Query= YW621_D08
Length=266
? Score E
Sequences producing significant alignments: ? (Bits) Value
NC_000017.11:c44389649-44372181Homosapienschromosome17_ITGA2B_7co...? 329 5e-92
NC_000017.11:c44389649-44372181Homosapienschromosome17_ITGA2B_7co...? 329 5e-92
>NC_000017.11:c44389649-44372181Homosapienschromosome17_ITGA2B_7core,GRCh38.p13PrimaryAssembly
Length=17469
Score = 329 bits (178),? Expect = 5e-92
Identities = 179/180 (99%), Gaps = 0/180 (0%)
Strand=Plus/Minus
Query? 1 GCCTTTCTKAGGTCCCAGATCCTTTAAGGCCCATGCCCTCTGCCTCCTCACCAGCTCACG? 60
|||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 9315? GCCTTTCTGAGGTCCCAGATCCTTTAAGGCCCATGCCCTCTGCCTCCTCACCAGCTCACG? 9256
Query? 61 GGTGTCTTGGTCTGAGGTAGGACACAGCTCTTCACAGCAGGATTCAGTGAATCTTGCACC? 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 9255? GGTGTCTTGGTCTGAGGTAGGACACAGCTCTTCACAGCAGGATTCAGTGAATCTTGCACC? 9196
Query? 121? AGTAGCTGGACAGAGGCCTTCACCACTGGCTGAGCTCTGATGGGATAGGGTGATGGGGTA? 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 9195? AGTAGCTGGACAGAGGCCTTCACCACTGGCTGAGCTCTGATGGGATAGGGTGATGGGGTA? 9136
>NC_000017.11:c44389649-44372181Homosapienschromosome17_ITGA2B_7core,GRCh38.p13PrimaryAssembly
Length=1773
Score = 329 bits (178),? Expect = 5e-92
Identities = 179/180 (99%), Gaps = 0/180 (0%)
Strand=Plus/Minus
Query? 1 GCCTTTCTKAGGTCCCAGATCCTTTAAGGCCCATGCCCTCTGCCTCCTCACCAGCTCACG? 60
|||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 632? GCCTTTCTGAGGTCCCAGATCCTTTAAGGCCCATGCCCTCTGCCTCCTCACCAGCTCACG? 573
Query? 61? GGTGTCTTGGTCTGAGGTAGGACACAGCTCTTCACAGCAGGATTCAGTGAATCTTGCACC? 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 572? GGTGTCTTGGTCTGAGGTAGGACACAGCTCTTCACAGCAGGATTCAGTGAATCTTGCACC? 513
Query? 121? AGTAGCTGGACAGAGGCCTTCACCACTGGCTGAGCTCTGATGGGATAGGGTGATGGGGTA? 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 512? AGTAGCTGGACAGAGGCCTTCACCACTGGCTGAGCTCTGATGGGATAGGGTGATGGGGTA? 453
Lambda ? K H
1.36 0.630 1.15
Gapped
Lambda ? K H
1.28 0.460 0.850
Effective search space used: 101888816
Query= YW665_C09
Length=307
? Score E
Sequences producing significant alignments: ? (Bits) Value
NC_000007.14:80602207-80679277Homosapienschromosome7_CD36,GRCh38....? 416 5e-118
NC_000007.14:80602207-80679277Homosapienschromosome7_CD36_core,GR...? 416 5e-118
>NC_000007.14:80602207-80679277Homosapienschromosome7_CD36,GRCh38.p13PrimaryAssembly
Length=77071
Score = 416 bits (225),? Expect = 5e-118
Identities = 228/229 (99%), Gaps = 1/229 (0%)
Strand=Plus/Plus
Query? 1 ? TAGGTCAATCTATGCTGTATTTGAATCCGACGTTAATCTGAAAGGAATCCCTGTGTATAG? 60
? ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 68768? TAGGTCAATCTATGCTGTATTTGAATCCGACGTTAATCTGAAAGGAATCCCTGTGTATAG? 68827
Query? 61 ATTTGTTCTTCCATCCAAGGCCTTTGCCTCTCCAGTTGAAAACCCAGACAACTATTGTTT? 120
? ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 68828? ATTTGTTCTTCCATCCAAGGCCTTTGCCTCTCCAGTTGAAAACCCAGACAACTATTGTTT? 68887
Query? 121 CTGCACAGAAAAAATTATCTCAAAAAATTGTACATCATATGGTGTGCTAGACATCAGCAA? 180
? ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 68888? CTGCACAGAAAAAATTATCTCAAAAAATTGTACATCATATGGTGTGCTAGACATCAGCAA? 68947
Query? 181 ATGCAAAGAAGGTGAGTAAATAACCTCAGTAGCACAG-CCATACCATAA? 228
? ||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct? 68948? ATGCAAAGAAGGTGAGTAAATAACCTCAGTAGCACAGTCCATACCATAA? 68996
>NC_000007.14:80602207-80679277Homosapienschromosome7_CD36_core,GRCh38.p13PrimaryAssembly
Length=1580
Score = 416 bits (225),? Expect = 5e-118
Identities = 228/229 (99%), Gaps = 1/229 (0%)
Strand=Plus/Plus
Query? 1 TAGGTCAATCTATGCTGTATTTGAATCCGACGTTAATCTGAAAGGAATCCCTGTGTATAG? 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 865? TAGGTCAATCTATGCTGTATTTGAATCCGACGTTAATCTGAAAGGAATCCCTGTGTATAG? 924
Query? 61 ATTTGTTCTTCCATCCAAGGCCTTTGCCTCTCCAGTTGAAAACCCAGACAACTATTGTTT? 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 925? ATTTGTTCTTCCATCCAAGGCCTTTGCCTCTCCAGTTGAAAACCCAGACAACTATTGTTT? 984
Query? 121? CTGCACAGAAAAAATTATCTCAAAAAATTGTACATCATATGGTGTGCTAGACATCAGCAA? 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct? 985? CTGCACAGAAAAAATTATCTCAAAAAATTGTACATCATATGGTGTGCTAGACATCAGCAA? 1044
Query? 181? ATGCAAAGAAGGTGAGTAAATAACCTCAGTAGCACAG-CCATACCATAA? 228
||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct? 1045? ATGCAAAGAAGGTGAGTAAATAACCTCAGTAGCACAGTCCATACCATAA? 1093
Lambda ? K H
1.35 0.626 1.14
Gapped
Lambda ? K H
1.28 0.460 0.850
Effective search space used: 118733338
? Database: refdata.fasta
Posted date:? Nov 12, 2019? 3:50 PM
? Number of letters in database: 411,130
? Number of sequences in database:? 16
Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5