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cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters

Authors: Gilchrist, Cameron; Booth, Thomas J; van Wersch, Bram; van Grieken, Liana; Medema, Marnix H; Chooi, Yit-Heng;

cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters

Abstract

This release resolves some long standing bugs and adds support for searching against the ClusteredNR database. What's Changed Initial support for searches against the ClusteredNR database (NR database clustered at 90% identity). To enable, specify nr_cluster_seq as a database when performing remote mode searches, e.g.: cblaster search -qf query.fasta -m remote -db nr_cluster_seq. This should give significantly faster remote searches compared to the regular NR database (which remains the default). Note that query sequences are only searched against NR cluster representative sequences; clusters are then expanded to include other sequences in the cluster, and hit data (identity, coverage, evalue, bitscore) for all member sequences are taken from the representative hit. Don't add empty sequences to DB so diamond does not fail by @biobeni in https://github.com/gamcil/cblaster/pull/122 Fix GenBank parsing when first gene wraps chromosome start/end by @biobeni in https://github.com/gamcil/cblaster/pull/121 Fix missing database and empty .fasta file error by @kaileyhh in https://github.com/gamcil/cblaster/pull/111 Lowered default hitlist size to 500 to avoid BLAST result errors Fixed search bug caused by query sequence headers containing whitespace New Contributors @biobeni made their first contribution in https://github.com/gamcil/cblaster/pull/122 @kaileyhh made their first contribution in https://github.com/gamcil/cblaster/pull/111 Full Changelog: https://github.com/gamcil/cblaster/compare/v1.3.20...v1.4

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