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GCG NUTS and BOLTS

There are a few GCG utilities that can help make manipulations MUCh easier.

  • Sequence Input/Editing

    • GETSEQ:  copy sequence from anywhere, paste it into a GCG format file

    • SEQED:  edit a GCG format file (beware, this is the vi editor thinly veiled)

  • Getting Output

    • LISTFILE filename will print your UNIX testfile to your local printer port (works in the student lab)

    • ftp the file to the local machine and use simpletext or Word

  • Sequence Output

    • MAP is a handy way to output  a sequence and to examine its translations

    • PUBLISH is a way to get a publication quality output that is very flexible

    • MAPSORT/MAPPLOT is the way to get a graphic output of a restriction map

  • Sequence Manipulation

    • REVERSE can do reverse complement, but it can also do reverse (in the event that you ever enter a sequence 3'-5' by accident)

    • SHUFFLE randomizes sequences, which can be handy in alignment comparisons, etc.

    • COMPOSITION tells you the nucleotides, dinucleotides, and trinucleotides or amino acids

    • FINDPATTERNS is a great search utility on a sequence

    • Reformat functions include FromGenbank, FromFASTA, FromEMBL and ToFASTA, etc.

 

University of KentuckyMorgan School of Biological SciencesNSF-CCD Support wpe1.jpg (5798 bytes)Chuck Staben, copyright reserved || 10/08/98