blast -m1

当database是10个物种(A、B、C、E、F、G、H、J、I、K)时,进行all vs all 比对结果是:

此时reference是物种A的第一个基因:即用10个物种的genome中的所有基因比对物种A的基因1

eg:如下

$ cat A_R00001_A.fa.70.blastp.m1|grep '1_0' -A 2 > r.sh

Query= A_R00001_A
         (423 letters)

Database: all.10
           165,229 sequences; 72,505,122 total letters

Searching..................................................done



                                                                                     Score    E
Sequences producing significant alignments:                                          (bits) Value                                   

A_R00001_A                                                                            855   0.0
B_R00001_B                                                                            766   0.0


1_0 1 PITLWLFYTHWLPGSPTTHHRVQGTTAMKDMVKCRVLKAHPCQECGKSFSKKGNLKRHQR 60 A_R00001_A 1 ............................................................ 60 B_R00001_B 4 ..l.......w..dAA....L..rv......................... 53 -- ... 1_0 361 GKCFPHKRHLIKHQLLHSRGGAYKCGVCGKRYRLKKYLRRHQKIHMREGTAPCSKPGYTT 420 A_R00001_A 361 ............................................................ 420 B_R00001_B 357 ..........................d..................t.........wee.. 416 -- 1_0 421 QTA 423 A_R00001_A 421 ... 423 B_R00001_B 417 R.G 419

 

1.Sequences producing significant alignments:大致情况,并计算score值,E值

关于score值:

he bit score gives an indication of how good the alignment is; the higher the score, the better the alignment. In general terms, this score is calculated from a formula that takes into account the alignment of similar or identical residues, as well as any gaps introduced to align the sequences.

2.具体情况,

1_0:表示reference的的第一个基因,即A物种的基因1

B_R00001_B:表示物种B的基因1与该reference(A物种的基因1) 的比对情况,从第4个AA开始到第53个AA结束

..l.......w..dAA....L..rv........................长度为53-4+1=50个;.是比对成功;空白是B物种基因1没有序列;60个为一组

如果物种A有10个基因,则将会把10个基因全部比对一遍:

$cat A_R00001_A.fa.70.blastp.m1|grep 'Query' >> r.sh

Query= A_R00001_A
Query= A_R00002_A
Query= A_R00003_A
Query= A_R00004_A
Query= A_R00005_A
Query= A_R00006_A
Query= A_R00007_A
Query= A_R00008_A
Query= A_R00009_A
Query= A_R00010_A

 

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转载自www.cnblogs.com/yuanjingnan/p/11316987.html
m1