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Unfinished Consensus

This type of consensus, when written in staden format, consists of a,c,g,t for single stranded regions and d,e,f,i for finished sequence (d=a,e=c,f=g,i=t). For fasta format the d,e,f,i are converted to n's. These files could be used for screening purposes. i.e. only single stranded regions would produce hits. Contigs can be selected from a file of file names or a list and output can be in fasta or staden formats.

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The contigs for which to calculate a consensus can be a particular "single" contig, "all contigs", or a subset of contigs whose names are stored in a "file" or a "list". If a file or list is selected the browse button will be activated and if it is clicked an appropriate browser will be invoked. If the user selects "single" then the dialogue for choosing the contig and the section to process becomes active.

The "strip pads" option will remove pads ("*"s) from the consensus sequence.

The routine can write its consensus sequence in "fasta" and "staden" formats. The output file can be chosen with the aid of a file browser.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_119.html