sequencig.. basic help :)

James VanEe jiv2 at cornell.edu
Mon Dec 18 09:13:48 EST 2000


SCF:
http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_2.html
http://www.mrc-lmb.cam.ac.uk/pubseq/scf-rfc.html

ABIF:
http://www.cs.cmu.edu/~genome/Papers/clark.html

If you want a sample ABIF file, you can log into our core lab's 
results distribution system 
(http://brcweb.bio.cornell.edu/seqresults.html) with
name: control
password: 000000

Software that can open an ABIF file and then save it as SCF: 
http://www.technelysium.com.au/chromas.html

I think what you're trying to do is sequence assembly.  Sequencing 
reactions generate relatively short reads from a longer template. 
Software is then used to find the overlapping regions of the short 
reads and "assemble" them to reconstruct the full sequence. There are 
many strategies for doing this. (note: That is very simplified, in 
the real world there's a lot of molecular biology and experimental 
design leading up to the sequence generation).

the phred/phrap/consed set of programs: 
http://www.genome.washington.edu/UWGC/methods.htm

some components of the staden package: http://www.mrc-lmb.cam.ac.uk/pubseq/

There are many other programs including commercial software (I 
hesitate to produce an incomplete of the commercial stuff here. The 
software above is free for academics).

other resources for learning about sequencing and the associated 
informatics would include the archives of this newsgroup (and the 
other bionet newsgroups dealing with software 
http://www.bio.net/archives.html) and those of the Association of 
Biomolecular Resource Facilities 
(http://abrf.org/archives/hmail/index.html) there is lots of other 
information out there.
good luck,
-James




>hi,
>
>I have to write a program that sequences a piece of dna. Our task was to
>randomly generate a chain of nucleotids, split two copies of this chains
>with enzymes and reconstruct the original dna-fragment out of these pieces.
>But I wanted to improve the program by making it ready for real sequencing.
>I read a primer on molecular genetics and already have little little
>knowledge about what I'm doing. Maybe someone of you might explain to me the
>problems of sequencing? Another question... where to get information about
>the ABI and SCF file format, and can I get example files somewhere?...
>
>bye bye...

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James VanEe                              Phone: (607) 254-4862
BioResource Center
Computing Facilty
170/171 Biotech Bldg                       Fax: (607) 254-4847
Cornell University
Ithaca, NY 14853                 www: http://brcweb.bio.cornell.edu
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