How come Alignment length is longer than Subject sequence length?

Question

[jth6974]

I just get a result of blastp. and The result is like below,

99.2 1880 2361 1882 13 0 3820 (Identical matches(%), Query Length(aa), Subject Length(aa), Alignment Length(aa), Number of gap openings, e-value, bitscore)

How can it is possible? Is this because of the gap openings?

Answer 1

[h.mon]

Yes, it is because of the gap openings. You can check yourself with a quick experiment: blast a sequence against itself, then delete some bases from the sequence, and blast against the original sequence. For example, a transcript of size 1128 bases the RCAN1 gene against itself:

NM_001331016.1    NM_001331016.1    100.000    1128    0    0    1    1128    1    1128    0.0    2084

Now the same transcript, but with 10 randomly deleted bases:

NM_001331016.1    NM_001331016.1     99.113    1128    0    10    1    1118    1    1128    0.0    2019

[jth6974]

thanks!!! so nice example!!

[jth6974]

but I want to explain about similarity using a table including Identity and Query coverage. If Query length = 497, Aln length = 531 and make a table with this, Query coverage is 100%? or 107%? cause if I write "Query coverage = 107%" in thesis, I think it might make people confused! How can I explain about this well and make table with this?

[h.mon]

In this case, the alignment can not cover more than 100% of the query, even though the alignment length can be longer than the query length. If people get confused, they will ask about this at your defense, and you can explain it nicely then. You can also put an explanatory footnote at the table.

Answer 2

[shubhra.bhattacharya]

This can be because there can be gapped alignments occuring or gaps in your sequence.