
22-Jan-2014

fasta36/scripts

Perl scripts for annotating sequences and expanding libraries

-- Sequence alignment annotation

All of the "ann_*.pl" scripts are used to annotate query or library
sequences using the -V option.  See ../test/test2V.pl for examples.

ann_feats2ipr.pl -- generate Uniprot sites, Interpro domains, from a mySQL database

ann_feats2l.pl -- generate Uniprot sites, domains from a mySQL database

ann_feats_up_www2.pl -- generate Uniprot sites, domains from an EBI
		     	web server that converts Uniprot DAS to gff3.

ann_feats_up_www.pl -- generate Uniprot sites, domains from a Uniprot
		       gff web server (less information than ann_feats_www2.pl)

ann_pdb_cath.pl -- generate CATH domains using PDB accessions from a mySQL database

ann_pfam.pl -- generate Pfam domains using local Pfam mySQL database

ann_pfam_www.pl -- use Pfam Website, and XML::Twig, to get Pfam domain info.

-- Library expansion

expand_uniref50.pl -- allows search of uniref50 to be expanded
expand_links.pl -- script to take hits from a smaller library and expand to complete library
links2sql.pl -- create links for expand_links.pl

exp_up_ensg.pl -- expand uniprot sequences to include Ensembl splice variants

-- Plot local alignments (.lav files)

lav2plt.pl    -- used to produce postscript or svg plots of "lalign36 -m 11" lav output files
color_defs.pl -- used by lav2plt.pl to produce domain colors
lavplt_ps.pl  -- used by lav2plt.pl --dev ps
lavplt_svg.pl -- used by lav2plt.pl --dev svg

