Debian software which allows searching nucleotide / amino acid sequence and showing intron/exon boundries or begin/termination of translations

[Mark Farnell <mark.farnell@gmail.com>]

Hi!

One can use pubmed nucleotide easily for searching DNA sequences for a
particular gene.  However is there any website / debian software which
also shows other information such as intron/exon boundaries, beginning
/ end of transcriptions?  For aa sequences, to show the boundries of
exons.

Also, is there any Debian program which can automate design of primers
for different purposes?

e.g. PCR of genomic DNA: primers in intron

RT-PCR: primers must bind to cDNA only, therefore one or both primers
spans across the boundries of two exons.  Also, amplification regions
must be as close to poly-A tail as possible after  following the
previous rule, so that if cDNA breaks, the breaks are less likely to
be within the amplified region

Thanks for your help!

Mark