SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Standalone BLAST output MattN Bioinformatics 8 02-01-2015 11:17 PM
Standalone blast jomaco Bioinformatics 3 11-26-2011 07:02 AM
Help with standalone blast Ami General 0 09-07-2010 01:37 AM
Help with Standalone Blast Ash Bioinformatics 2 08-23-2010 05:14 AM
StandAlone Blast+ weird response BioSlayer Bioinformatics 8 08-17-2010 12:48 AM

Reply
 
Thread Tools
Old 01-31-2012, 06:24 AM   #1
jomaco
Member
 
Location: Sheffield

Join Date: Oct 2011
Posts: 26
Default Standalone Blast output

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
jomaco is offline   Reply With Quote
Old 01-31-2012, 07:18 AM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 836
Default

Quote:
Originally Posted by jomaco View Post
<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.

Quote:
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".
gringer is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:04 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO