Blast subject coordinates

Question

[deepti1rao]

It might be a silly question. But please do clear my doubts.

1. What do the subject coordinates in the blast alignment represent? They don't appear to be genomic coordinates to me. Are they coordinates of the accession?

2. How can I extract the exact genomic coordinates for a hit?

Answer 1

[Ram]

Blast compares the sequence you input, called the query to each sequence in a database. The database sequences are called subjects. Because it is a local alignment search, part of the query matches part of the subject. The better the match, the better the score. The coordinate of the subject sequence where the local match begins is the subject coordinate.

The way to extract genomic co-ordinates would be to map the subject sequence to its genomic coordinates and use the subject match coordinate (explained above) as an offset. For example, if match happens at subject:120, and subject starts on chr3:10000000, then your hit starts at chr3:10000000+120 = chr3:10000120