ggavelis Goto Github PK
Name: Greg Gavelis
Type: User
Company: Bigelow Laboratory for Ocean Science
Bio: Greetings, here you'll find sample code that I'm migrating from across my institutional GitHub accounts.
Location: Boothbay, Maine
Name: Greg Gavelis
Type: User
Company: Bigelow Laboratory for Ocean Science
Bio: Greetings, here you'll find sample code that I'm migrating from across my institutional GitHub accounts.
Location: Boothbay, Maine
InterProScan is useful, but its annots are multiline and redundant. This collapses them into a single, human-readable line for each annotated sequence.
How can we discriminate contaminants from HGT? Alien indices are often used to screen out foreign sequences, but can 'overclean' by removing bona fide HGT. This script leverages metadata about each DNA/AA sequence (i.e. whether it is spliced, has a polyA tail or spliced leader), and uses that to assess the extent to which AI-based cleaning is removing legitimate HGT.
Did you know that Trinity predicts splice variants? (Chrysalis works even for de novo transcriptomes, and its input--though heuristic--is valuable). Likewise, TransDecoder can predict multiple ORFs per protein--potentially capturing alternative splicing. These predictions are usually lost once we rename our proteins to shorter seqids. This script stores and abbreviates potential splicing info for later use--e.g. for discerning prokaryotic from eukaryotic transcripts.
Tools to add phylogeny-ready names (including accession, genus, species, lineage & taxid) to protein fastas from any of (A) genbank (B) SRA (C) Genome_paper_supp_data
Need an ORF from an unannotated genome? This script exploits ncbi's ability to tBLASTn against genome assemblies, to get provisional exon sets from BLAST query-hit alignments.
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