transcript and fasta sequence
Hello all! I have two file containing ten thousands of transcripts fasta sequences each with different ids and I am interested in finding common sequences between the two files. Somebody please help me as it is hindering my work. Thank you in appreciation
1 answer
Hello qudrat,
If you are interested in IDENTICAL sequences, you can simply write a very short script to extract identical sequences in both files.
You want to apply a "similarity" score, if so I strongly suggest using multi-aligners (BLAST or MUSCLE for instance) and then parse the results to have a global overview of similarity between sequences from your two different files.
EDIT @genomax commentary: Use of assembly merge-tool.
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In what way?
How about this tool that merges assemblies? See more options here: High quality de novo transcriptome assembly rely on merging multiple assembly? Specifically
dedupe.shfrom BBMap should be very simple to use.Can you post an example? Is this a de novo assembly?
Actually this a de novo assembly produced by using two different softwares to minimizes the false positives