[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

I seek your technical help / advice about using needle / stretcher for my
purposes, explained briefly below:


   - 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

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,
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