I am working on MicroRNA seq data analysis. I have completed the preprocessing steps and blastn search was performed against plant miRNAs from miRBase. The output of blastn search was an xml file. Now I need to analyse this xml file to identify conserved and novel MicroRNAs. Could someone please suggest how this can be done.
Hello,
I would recommend you, to run the blast again using output format as tab delimited format. It will be easy for you to parse the results. I would also recommend you, to use word size 7, because you are using short sequences. Hope this will help.
You could run a blastn against mirBase microRNAs with this command:
$blastProg -db $blastDB -query $inFile -word_size 7 -out $outFile -outfmt "10 qseqid sallseqid qstart qend sstart send qseq sseq length pident nident mismatch gaps evalue" -num_threads $nbThread
(http://www.ncbi.nlm.nih.gov/books/NBK279675/)
The output is a csv file with the filds specified in -outfmt. It's simple to parse. You don't need Bioperl or Biopython to do it.
A candidate microRNA is a sequence that respects some cutoffs like: identity percentage, query coverage, subject coverage, gaps, totale mimatches. and length.
You need to calculate the number of total mismatches: internal mismatches + external mismatches + internal gaps + external gaps.
internal mismatches and gaps are in the blast output but you need to calculate the external ones.
Thanks a lot Mohamed Remita and Suyash Agarwal for your valuable suggestions
Thanks for the suggestions and it helped me to sort the problem. I have set the option -outfmt 6 and got the Blastn output in tabular form with 12 column headers.
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