Question: How come Alignment length is longer than Subject sequence length?
0
gravatar for jth6974
23 months ago by
jth697410
jth697410 wrote:

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?

blastp blast alignment • 1.4k views
ADD COMMENTlink modified 23 months ago by h.mon31k • written 23 months ago by jth697410
4
gravatar for h.mon
23 months ago by
h.mon31k
Brazil
h.mon31k wrote:

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
ADD COMMENTlink modified 23 months ago • written 23 months ago by h.mon31k

thanks!!! so nice example!!

ADD REPLYlink written 23 months ago by jth697410

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?

ADD REPLYlink modified 23 months ago • written 23 months ago by jth697410

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.

ADD REPLYlink written 23 months ago by h.mon31k
1
gravatar for shubhra.bhattacharya
23 months ago by
shubhra.bhattacharya120 wrote:

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

ADD COMMENTlink modified 23 months ago • written 23 months ago by shubhra.bhattacharya120
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