Fast visualisation of BLAST search hits' annotations

Question

[Andrés Ribone]

Hello, I'm new in bioinformatics. I have (I think) a very silly issue:

Doing a web based NCBI BLAST search against nr/nt database; when you get as a hit a fragment from a contig or a complete genome assembly, regardless that fragment is well annotated inside the entire sequence (as a well known gene or whatever), you only see, for example, "Pityopsis falcata, partial genome" as the hit title.

That bothers me. I have to click in the sequence ID and search the fragment position to find out how was annotated that stupid sequence. I feel like an idiot making so many clicks.

Like I said, my "problem" is silly, but there has to be a solution.

Thanks in advance!

[h.mon]

Try blasting against refseq database.

Answer 1

[Pierre Lindenbaum]

I've written something like this for an old post: Aligning Two Proteins With Their Domains/Annotations see

https://github.com/lindenb/jvarkit/wiki/Biostar3654

$ cat ~/jeter.blastn.xml 

http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
(...)
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gi|14971104|gb|AF338247.1|</Hit_id>
  <Hit_def>Human rotavirus A strain M clone M1 NSP3 genes, complete cds</Hit_def>
  <Hit_accession>AF338247</Hit_accession>
  <Hit_len>2032</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_num>1</Hsp_num>
```

```
$ java -jar dist/biostar3654.jar ~/jeter.blastn.xml 2> /dev/null  | cut -c-${COLUMNS} 

QUERY: No definition line
       ID:Query_186611 Len:980
>Human rotavirus A strain M clone M1 NSP3 genes, complete cds
 AF338247
 id:gi|14971104|gb|AF338247.1| len:2032

   e-value:0 gap:0 bitScore:1764.98

QUERY 000000001 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGC 000000050
                ||||||||||||||||||||||||||||||||||||||||||||||||||
HIT   000000001 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGC 000000050
                ################################################## source organi
                ##################################                 5'UTR
                                                  ################ CDS codon_sta

QUERY 000000051 AGATGGTAAGCTCTATTATTAATACTTCTTTTGAAGCTGCAGTCGTTGCT 000000100
                ||||||||||||||||||||||||||||||||||||||||||||||||||
HIT   000000051 AGATGGTAAGCTCTATTATTAATACTTCTTTTGAAGCTGCAGTCGTTGCT 000000100
                ################################################## source organi
                ################################################## CDS codon_sta
(...)