Mode for DNA sequence editing

Thomas Sicheritz thomas at beagle.bmc.uu.se
Sat Apr 25 08:08:10 EST 1998


Another elisp dna-mode  is XEmacs's Bio-mode available at 
Molecular Linux http://evolution.bmc.uu.se/~thomas/mol_linux/index.html
with following functions:

bio-translate-region translates the marked nucleotide sequence 
bio-reverse-region returns the inverted sequence 
bio-antiparallel-region returns the reverse complementary nucleotide sequence 
bio-complement-region returns the complementary nucleotide sequence 
bio-readseq Reads a sequence file via a readseq pipe, and discards all newlines 

bio-convert-embl2-gtf converts an EMBL file to Gene Table Format (GTF) 
bio-embl-extract extracts all translation parts of an EMBL file 

bio-blast-on-region sends the marked sequence against the blast database 
bio-search-forward Search forward from point for oligo.(e.g. TAY will find TAC, TAT and TAY) 
bio-gccontent-on-region Calculates the G+C content in the marked region 
bio-ATrich-over-GCrich-codons Calculates the ratio of amino acids coded for by AT-rich codons over amino acids coded for by GC-rich codons 
bio-seqinfo returns Length, G+C overall, G+C at third pos., nt-frequency and AC/GC-codons 
bio-every-triplet Apply a function to each triplet of sequence, and make a list of the results 

Bio-mode is written for XEmacs - so I don't know if its working in Emacs ...
It's my first lisp programming attempt - so all suggestions are welcome !

-thomas

-- 
Sicheritz Ponten Thomas E.  Department of Molecular Biology
Biomedical Center           Uppsala University
BMC:  +46 18 4714214        BOX 590 S-751 24 UPPSALA Sweden
Fax   +46 18  557723        http://evolution.bmc.uu.se/~thomas
Molecular Tcl:   http://evolution.bmc.uu.se/~thomas/tcl
Molecular Linux: http://evolution.bmc.uu.se/~thomas/mol_linux
 
	De Chelonian Mobile ... The Turtle Moves ...





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