Script for extracting genes ?

Thomas Sicheritz thomas at evolution.bmc.uu.se
Tue Jul 9 06:49:38 EST 1996


Hej,

I need a script/program which can scan an EMBL or Genbank file and
extract all gene names with start-stop, length, type, direction ...
(maybe exon information too)

the output should be something like that: 
rice chloroplast:
name      type         dir      start   stop    length
rps16:x2:2      CDS     R       4487    4635    148
rps16:x1:2      CDS     R       5514    5553    39
trnQ    tRNA    R       6615    6687    72
psbK    CDS     F       7033    7218    185
psbI    CDS     F       7608    7718    110
trnS    tRNA    R       7829    7916    87
ORF100  CDS     F       8349    8651    302

has anybody seen or written such a script/program (in perl,tcl,C,C++) ?

thx
-thomas


Sicheritz Ponten Thomas E.              UPPSALA UNIVERSITY 
Vangsbyvaegen 128   S-740 20 Vaenge     Biomedical Center
Home: +46 18  364358                    Department of Molecular Biology
BMC:  +46 18  174379                    BOX 590 S-751 24 UPPSALA Sweden
Fax   +46 18  557723                    http://skydancer.bmc.uu.se/~thomas
 
        Chaos always defeats order, 
                because it is better organized.
                                               (Terry Pratchett)




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