can anyone explain pipes in blastn output

Question

[barvazduck]

Hi All,

Can anyone explain what does all the pipes and letters mean in the blastn (local blast, ncbi-blast+ on linux terminal)?

are those alternatives to the main solution?

Query_1  1381   GGCAATGCGGTGAACGCCATGTCTACCTATCTTCCCGTGCAAGACGGGACGTACCATCAG  1440
178688   9271   GGCAATGCGGTGAACGCCATGTCTACCTATCTTCCCGTGCAAGACGGGACGTACCATCAG  9330
97017    10239  --CAATGCGGTGAACGCCATGTCCGCATATCTTCCCGTGCAAGACGGGACGTACCATCAA  10173
                                            \ \\\   \                       
                                            | |||   |                       
                                           TT GAAT  C
                                               ||                           
                                               C|
                                                |                           
                                                C

Thanks,
Raz

[GenoMax]

Formatting is making it hard to see what is being represented in the "code" part. What output format option was used to get this?

[barvazduck]

-outfmt 1

What is the problem with formatting? I can see clearly on my computer.

[Anima Mundi]

I think it just depends on the size of your monitor. Adjusting the zoom should allow you to visualise the alignment properly.

Answer 1

[GenoMax]

Not sure if this link will come through but here goes: https://books.google.com/books?id=zDqksXUaoBAC&pg=PT312&lpg=PT312&dq=query-anchored+showing+identities

The representation may have changed with blast+ since the book refers to the older version of blast. Checking to see what the new outfmt '1' looks like now.

[barvazduck]

Great thanks!!

these are insertions that do not occur in the query seq. it became clear when I used outfmt 3