#______________________________________________________________ # Title : fetch.pl # Usage : fetch.pl SWISS_ENTRY # # Function : fetches swissprot entry or fasta format seq with # given seq name(like SAA_HORSE, SA*HORSE, SAA,..) # you can give multi files(SAA*, SAU*) at the same # time. This uses ENV setting of 'SWDIR'. # If you already know where you put seq.dat you can # specify in the prompt. jong@mrc-lmb.cam.ac.uk # # Example : fetch.pl YAPT, fetch.pl *YEAST # # Keywords : fetch_swissprot_sequence, fetch_sequence, # find_swiss_sequence, find_sequence # # Options : _ for debugging. # # for debugging. # -f for fasta format file output # -a is for ALL matched seq. (same as using glob=> *YEAST) # -c is for Creating seq.idx file # -h is for HELP! # -g is for GDF file format output # -l is for list of match entries(in 1 column) # -s is for species option (input name mst be species (YEAST, RAT, HUMAN..) # n= is for Number of seq you want to get from swissprot # s= is for Size limit. Min seq size in swiss, s=10 -> minimum 11 aa seq. # S= is for Size limit. Max seq size in swiss, s=1000 -> get less than 1000 # # Returns : STDOUT # Argument : swissprot seqname # Version : 1.6 #-------------------------------------------------------------- ftp site: ftp.mrc-lmb.cam.ac.uk /pub/genomes/Software/Fetch