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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