blast -m1

Posted 2022-06-17 yuanjingnan

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