Standalone Blast output

[jomaco]

Hi

When looking at the output from standalone blast I see this:

<Hsp_hit-from>76056</Hsp_hit-from>
<Hsp_hit-to>76901</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>3</Hsp_hit-frame>
<Hsp_identity>89</Hsp_identity>
<Hsp_positive>141</Hsp_positive>
<Hsp_gaps>19</Hsp_gaps>
<Hsp_align-len>286</Hsp_align-len>

Can anyone tell me why is the align length less than "hit-to" minus "hit-from"?

Is there a description of the output available anywhere, maybe I am looking at this wrongly. Hope you can help

Thanks

[gringer]

<Hsp_hit-from>76056</Hsp_hit-from>
<Hsp_hit-to>76901</Hsp_hit-to>
...
<Hsp_gaps>19</Hsp_gaps>
<Hsp_align-len>286</Hsp_align-len>

Can anyone tell me why is the align length less than "hit-to" minus "hit-from"?

It looks like there are 19 gaps in the alignment (Hsp_gaps is non-zero), which will contribute substantially to the align length being shorter than the hit range.

Is there a description of the output available anywhere

ftp://ftp.ncbi.nlm.nih.gov/blast/doc...l/README.blxml

Linked from the first google hit for "BLAST XML format".