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If you already know the basic sequence i.e. the fixed regions in the primer; for e.g. the known nucleotides in the sequence - NGATWGCTSATNGC, then you can implement your algorithm like this: Fix the max length of the primers. Lets say 20nt. Generate all combinations of primers (20nt): that is pretty straightforward. You will have 4N × 2(R+Y+S+W+K+M) × ...


2

It means k-mer coverage. From the velvet manual: 4.2.1 The contigs.fa file This fasta file contains the sequences of the contigs longer than 2 k , where k is the word-length used in velveth. If you have specified a min_contig_length threshold, then the contigs shorter than that value are omitted. Note that the length and coverage ...


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http://phagesdb.org/phages/Bxb1/ here you can click "Locally BLAST this genome" it will give you the sequence in FASTA format and then you can click BLAST if you want additional information about the sequence, alignment, etc


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There exists a bunch of population genetics forward and backward (coalescence) simulation platforms. Here is a non-exhaustive list. They all differ and you'll have to go through their manual to see what is more adapted to your needs. Here is an exhaustive (or almost exhaustive) list of such platforms. Some are more known than others. Personally, I already ...



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