tblastx fmt1 Output Interpretation

[syintel87]

Hello,
While locally running "blastx" with output option "-outfmt 1", I have a question.

The below is an example of my result. As seen, throughout the outputs, all pairs of anchored proteins are not matched. How can I interpret these non-identical alignment?

Query_3 477 GSVEYVHMLNGTMCATTRTVCAL 409
medicagoRALF3 38 .GM.WI.QTKTAT.EGSIAD.M. 60

Query_4 34 PYHLLLQKFYKT 69
medicagoRALF11 104 ..NRGCS.Y.RC 115

Thank you in advance.

[GenoMax]

Are you searching with very short query sequences (like illumina reads)?

[syintel87]

My query sequences are contigs that are de novo assembled, some of which are short (e.g. 500) whereas others are very long (e.g. 100,000).

But database of blast is composed of several peptide proteins whose length is short (e.g. 44).

[GenoMax]

Have you tried to do the search the other way around (using your peptides as query)?

Try using BLAT too. Especially if you know that you expect the peptides to be there in your data.

[syintel87]

In addition to "-outfmt 1", I tried other options as well.
There seem to be different ways of alignment.

0 = pairwise
1 = query-anchored showing identities
2 = query-anchored no identities
3 = flat query-anchored, show identities
4 = flat query-anchored, no identities

[-outfmt 0]
Query_2 229 KMSFRYLFFAIKKYALSKF 173
thalianaRALF4 5 ...LTS...VSIVIV..L. 23

[-outfmt 1]
Query_2 229 KMSFRYLFFAIKKYALSKF 173
thalianaRALF4 5 ...LTS...VSIVIV..L. 23

[-outfmt 2]
Query_2 229 KMSFRYLFFAIKKYALSKF 173
thalianaRALF4 5 KMSLTSLFFVSIVIVLSLF 23

[-outfmt 3]
Query_2 229 KMSFRYLFFAIKKYALSKF 173
thalianaRALF4 5 ...LTS...VSIVIV..L. 23

[-outfmt 4]
Query_2 229 KMSFRYLFFAIKKYALSKF 173
thalianaRALF4 5 KMSLTSLFFVSIVIVLSLF 23

The results of [-outfmt 2] and [-outfmt 4] may be the results that I look forward to getting. However, I still cannot understand the principles and differences that distinguish output format 0 to 4.

[syintel87]

Ah, now I see! In formats "0, 1, and 3", dots stand for identities between query and target. And differences are shown with protein letters.

I should have posted after more consideration.
Thanks GenoMax! I am going to try "BLAT", too.