Entering edit mode
7.2 years ago
ashish
▴
680
I am using blast2go for which I did a local blast with output in .xml format. Now when I load these results in blast2go and start mapping, a lot of sequences does not map. however they are there in the blast output. I was thinking it has something to do with the parameters which blast2go asks to define before loading the blast output. these are 'separator', 'position' and 'join hit id and description'. can someone explain to me the meaning of these and what should be their values in my case. The xml output when opened in notepad looks like this.
<Hit_num>1</Hit_num>
<Hit_id>gi|357140705|ref|XP_003571904.1|</Hit_id>
<Hit_def>PREDICTED: protein RESTRICTED TEV MOVEMENT 2-like [Brachypodium distachyon] >gi|944061584|gb|KQJ97174.1| hypothetical protein BRADI_3g29220 [Brachypodium distachyon]</Hit_def>
<Hit_accession>XP_003571904</Hit_accession>
<Hit_len>334</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>233.032</Hsp_bit-score>
<Hsp_score>593</Hsp_score>
<Hsp_evalue>1.47757e-070</Hsp_evalue>
<Hsp_query-from>19</Hsp_query-from>
<Hsp_query-to>392</Hsp_query-to>
<Hsp_hit-from>25</Hsp_hit-from>
<Hsp_hit-to>333</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>0</Hsp_hit-frame>
<Hsp_identity>176</Hsp_identity>
<Hsp_positive>217</Hsp_positive>
<Hsp_gaps>97</Hsp_gaps>
<Hsp_align-len>390</Hsp_align-len>