The meaning of horizontal black lines and vertical black bars (lines) on NCBI's BLAST graphical output

Question

[User 0522]

Hi,

Could anyone guide me what do horizontal black lines and vertical black bars (lines) on NCBI's BLAST results graphical output denote?

Thanks indeed

Answer 1

[GenoMax]

If this document does not help then post an image indicating which lines you are referring to.
Guessing that you are referring to the pairwise alignment display of blast results, I am going to say that the vertical lines (between the query and subject bases) indicate identity. Horizontal lines in query or subject sequence indicate gaps inserted to get the alignment.

[english.server]

Thank you for your response. I did not find it either in NCBI help or the file you kindly provided. You may see the graph at:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=K40HH44J01R

I am sorry I could not post the image.

Thanks again.

[GenoMax]

Vertical black lines are denoting the boundaries of HSP.
From help text for the graphic from NCBI site.

This graphic is an overview of database sequences aligned to the query sequence. Alignments are color-coded by score, within one of five score ranges. Multiple alignments on the same database sequence are connected by a dashed line. Mousing over an alignment shows the alignment definition and score in the box at the top. Clicking an alignment displays the alignment detail.

[english.server]

Thank you for the response.

"Multiple alignments on the same database sequence are connected by a dashed line. " I also cant figure out why some sequences with 2 or >2 segments of similarity have a black line connecting them and some dont.

I would appreciate if you could help in this matter as well.