Phrap / Consed

Stefan Weckx sweckx at uia.ua.ac.be
Mon Jul 10 10:41:26 EST 2000

Hi all,

I've two questions about Phrap / Consed:
- it's possible to compile the Phrap "longreads/manyreads" version, and
it's also possible to compile gcphrap for the Staden package (with the
patch from the Staden website). Has anyone ever tried to combine these 2
ways of compiling, so that the longread/manyread version of Phrap can be
integrated into the Staden package? If so please let me know how!
- The *'s which appear in the consensus sequences in Consed are not
written in the fasta file with contigsequences generated by Phrap. Does
anybody know a possibility to get these *'s out of the consensus in
Consed (since these *'s get a basenumber in Consed which I want to
avoid) or to get them in into the fasta file with contigsequences?
Result must be a perfect match between the basenumbers in Consed and the
number of each base in the fasta file (if you would count them).

Stefan Weckx
Bioinformatics unit
Department of Molecular Genetics
University of Antwerp (UIA)		 

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net