Entering edit mode
10.9 years ago
pld
5.1k
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration>
element, as in the value of Iteration_iter-num
is one. For example:
http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>blastn</BlastOutput_program>
<BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version>
<BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference>
<BlastOutput_db>nr</BlastOutput_db>
<BlastOutput_query-ID>42945</BlastOutput_query-ID>
<BlastOutput_query-def>No definition line</BlastOutput_query-def>
<BlastOutput_query-len>1440</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_expect>10</Parameters_expect>
<Parameters_sc-match>1</Parameters_sc-match>
<Parameters_sc-mismatch>-2</Parameters_sc-mismatch>
<Parameters_gap-open>0</Parameters_gap-open>
<Parameters_gap-extend>0</Parameters_gap-extend>
<Parameters_filter>L;m;</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>42945</Iteration_query-ID>
<Iteration_query-def>No definition line</Iteration_query-def>
<Iteration_query-len>1440</Iteration_query-len>
<Iteration_hits>
.
.
.
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>20073013</Statistics_db-num>
<Statistics_db-len>50708408902</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>0</Statistics_eff-space>
<Statistics_kappa>0.46</Statistics_kappa>
<Statistics_lambda>1.28</Statistics_lambda>
<Statistics_entropy>0.85</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
So again, when running 1 sequence against a database of n sequences, I've only seen one <Iteration>
element. In what cases will there be multiple <Iteration>
elements? If I am only parsing results in from 1:n runs, can I assume that there will always only be one element?
So then yes, if I have one only one query sequence, I can assume that there will always be one
<Iteration>
object.