Gene_to_Sequences

Gene search pipeline for retrieving gene-coding nucelotide sequences and annotations from a local GenBank database.

This package is described in Rhee, S-Y and Shafer, RW (2017), "Geographically-Stratified Representative HIV-1 Group M pol Subtype and Circulating Recombinant Form Sequences," manuscript submitted for publication.

The package includes:

1. GB_to_BLASTDB.pl (a perl script) parses GenBank files, creates a fasta file with sequence headers containing GenBank annotations and converts the fasta file to a BLAST searchable databae.

2. Gene_to_Sequences.pl (a perl script) as the second part of the pipeline, it performs an amino acid to nucleotide sequence search for a gene and generates a file containing aligned full-length nucleotide sequences with associated GenBank annotations including AccessionID, Title, Authors, PubMedID, Country, Collection_Date and TaxonomyID

3. Subtree_Sampling.Rmd (a R markdown) samples subtype reference sequences from subtrees of a phylogenetic tree
   Usage guidelines for this R markdown

Prerequisites

• NCBI blast+
• BioPerl
• FASTA

Usage

For the usage

perl GB_to_BLASTDB.pl --help

perl Gene_to_Sequences.pl --help

For more information

perl GB_to_BLASTDB.pl --man

perl Gene_to_Sequences.pl --man

Authors

• Soo-Yon Rhee - Initial work - sooyonrhee

License

You may distribute this module under the same terms as perl itself