NCBI SRA blastn service

Never easier before to check your sequence against the NCBI Short Read Archive database:

NCBI SRA BLAST

First thoughts:

• Transcriptome coverage is hugely biased to the 3' end (or 5' depending on library preparation). A lot more than I suspected.
• Would be great to do queries for phylogenetic subclades: e.g. my human sequence against all SRA data for primates.
• A lot of the 454 data has homopolymer issues, mostly TTT[...]TTTs but also some others:
  

Query  465  GGGCCTTGACAAAGTGTAAACCGCATGGATGGGCTTCCCC-AAGGATTTATTGACATTGC  523<br /><font color="#ff0000"><b>Sbjct</b></font>  249  ........................................<font color="#ff0000"><b>C</b></font>...................  190<br /><br /></pre><ul><li>Some of these (unless they are real variations) get picked up as mismatches, some as indels:<pre>Query  1    CGGCAAGGTATGTGCGTGATTTTGGGCCCACGTGTATTTCCATTAATTTT-AAGCCGTAA  59<br /><font color="#ff0000"><b>Sbjct</b></font>  224  ..................................................<font color="#ff0000"><b>T</b></font>.........  165<br /><br />Query  60   TTGTCGTTTTTGGCGGTTTCGAGTTGAACTGCGTTAGTCCGTGCGCTGTTCGCAAGTGTG  119<br /><font color="#ff0000"><b>Sbjct</b></font>  164  ..........<font color="#ff0000"><b>C</b></font>.................................................  105<br /></pre></li></ul><pre><br />Query  61   TGTCGTTTTTGGCGGTTTCGAGTTGAACTGCGTTAGTCCGTGCGCTGTTCGCAAGTGTGC  120<br /><font color="#ff0000"><b>Sbjct</b></font>  118  .....<font color="#ff0000"><b>C</b></font>......................................................  177<br />Query  61   TGTCG-TTTTTGGCGGTTTCGAGTTGAACTGCGTTAGTCCGTGCGCTGTTCGCAAGTGTG  119<br /><font color="#ff0000"><b>Sbjct</b></font>  160  .....<font color="#ff0000"><b>T</b></font>...............................<font color="#ff0000"><b>-</b></font>......................  102<br />Query  61   TTAATTTTAAGCCGTAATTGTCGTTTTTGGCGGTTTCGAGTTGAACTGCGTTAGTCCGTG  120<br /><font color="#ff0000"><b>Sbjct</b></font>  181  ...........................<font color="#ff0000"><b>C</b></font>................................  122<br /><br /><br /><br />