Converting GCG Format
These files consist of one or more groups of non-blank lines separated by one or more blank lines; the non-blank lines look similar to this:
Chloroflex
Chloroflex Length: 428 Mon Sep 25 17:34:20 MDT 2000 Check: 0 ..
1 MSKEHVQTIA TDDVSKNGHT PPTNASTPPY PFVAIVGQAE LKLALLLCVV
51 NPTIGGVMVM GHRGTAKSTA VRALAAMLPP IKAVAGCPYS CAPDRTAGLC
101 DQCRALEQQS GKTKKPAVIN IPVPVVDLPL GATEDRVCGT LDIERALTQG
151 VQAFAPGLLA RANRGFLYID EVNLLEDHLV DVLLDVAASG VNVVEREGVS
201 VRHPARFVLV GSGNPEEGDL RPQLLDRFGL HARITTITDV SERVEIVKRR
251 REYDADPFAF VEKWAKETQK LQRKIKQAQR RLPEVILPDP VLYKIAELCV
301 KLEVDGHRGE LTLARA.ATA LAALEGRNEV TVQDVRRIAV LALRHRLRKD
351 PLETQD.... ...DAVRIER AVEEVLVP.. .......... ..........
401 .......... .......... ........
The “Check” tag near the end of a line signifies the first line in a new sequence expression. The name of the sequence is obtained from the preceding line; the following lines, up to the next blank line, are accepted as the sequence. For each line in the sequence, the leading digits are stripped off, and the rest of the line is used. The following shows a conversion of the above sequence.
#mega
Title: infile.gcg
#Chloroflex
MSKEHVQTIA TDDVSKNGHT PPTNASTPPY PFVAIVGQAE LKLALLLCVV
NPTIGGVMVM GHRGTAKSTA VRALAAMLPP IKAVAGCPYS CAPDRTAGLC
DQCRALEQQS GKTKKPAVIN IPVPVVDLPL GATEDRVCGT LDIERALTQG
VQAFAPGLLA RANRGFLYID EVNLLEDHLV DVLLDVAASG VNVVEREGVS
VRHPARFVLV GSGNPEEGDL RPQLLDRFGL HARITTITDV SERVEIVKRR
REYDADPFAF VEKWAKETQK LQRKIKQAQR RLPEVILPDP VLYKIAELCV
KLEVDGHRGE LTLARA.ATA LAALEGRNEV TVQDVRRIAV LALRHRLRKD
PLETQD.... ...DAVRIER AVEEVLVP.. .......... ..........
.......... .......... ........