[EMBOSS] run parameters for inexact matching with EMBOSS needle
Anandkumar Surendrarao
aksrao at ucdavis.edu
Sun Feb 3 12:18:33 UTC 2019
Dear EMBOSS users,
I recently discovered EMBOSS' needle and stretcher tools at
https://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html
and
https://www.ebi.ac.uk/Tools/psa/emboss_stretcher/nucleotide.html
respectively.
I seek your technical help / advice about using needle / stretcher for my
purposes, explained briefly below:
Context:
- I want to search with FASTA formatted DNA sequence queries that are <=
100nt in length,
- against FASTA formatted genomic DNA sequence,
- for global end-to-end matches (using Needleman Wunsch type global
search, not Smith Waterman type local matching)
- but allowing >= 80% identity and >= 80% of query length coverage
Is that possible with EMBOSS? If yes, what would be the appropriate run
parameters? I looked at
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needle.html, but
wasn't sure if there are run flags equivalent to blastN's -perc_identity
0.8 -qcov_hsp_perc 0.8, which is what I am trying to do. Could you please
help?
If it is not possible with EMBOSS suite tools, could you please suggest any
alternative tool and appropriate run parameters for it?
Thanks a lot,
Anand
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