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My follow up blog post BLAST max alignment limits repartee - part one introduces the small self-contained test case in this repository, and emphasises that this issue is not specific to -max_target_seqs but also affects the limits -num_descriptions and -num_alignments used with the human readable plain text or HTML output.
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The screen.seqs command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a names, group, contigsreport, alignreport and summary file. As an example, we will use the example from the Sogin data analysis example.
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GitHub - peterjc/blast_max_target_seqs: Reproducible test seqs seqs
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SEQS BACKGROUND The idea for the activities of the International Focus Group SEQS (Section on European Quaternary Stratigraphy, INQUA-SACCOM) started after several talks with Wim Westheroff, Guzel Danukalova and Markus Fiebig, particularly during the Nagoya 2015 INQUA Congress, and aims to continue and improve the SEQS’s past activities.
SEQS - What Does SEQS Abbreviation Mean?
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summary.seqs(fasta=stability.trim.contigs.fasta) screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxlength=570, minlength=400) unique.seqs(fasta=stability.trim.contigs.good.fasta)
Mothur dist.seqs output seqs seqs
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SeqS - omicX
SeqS is an easy to use Java-based tool that allows Fuzzy and Regular Expression searches on multiple sequences. It reads and uses sequences in FASTA format. Besides the stand-alone program, Sequence Searcher is also integrated in VOCS (Viral Orthologous Clusters).
The ‘-max_target_seqs’ parameter of NCBI BLAST may not do seqs seqs
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