the putative translations from the last Genbank release. You can
search GenPept using 'GenPept:*' in Fasta. In
Pileup,
you can then use the Begin= and End= parameters to define the ends of the
region for alignment. Each sequence can have its own
range
limitation.
Another option is to use
framesearch instead of fasta. You could then create a list file using the
begin, end and range information from the framesearch output, and use
that as input into Pileup. However, framesearch is much slower than Fasta.
How do I design a primer?
There are several design criteria:
- melting temperatures of primer and product
- GC content
- ambiguous bases
- self-complementarity -- how to avoid primer dimer formation and
primer secondary structure
- size of primer
- PCR product length
- repeats, e.g. similarity to common rodent repeat sequences
GCG's prime
program selects primers, and is also accessible through
GCG-Lite's
web interface to prime.
Other web-accessible primer design programs are
Primer3
from the Whitehead Institute,
xprimer from
U. Minnesota,
GeneFisher
from U. Bielefeld.
Programs than run on Macs
and PC's are
MacVector for the Mac,
GeneWorks
for the Mac,
OSP
for Mac/PC/VAX/Sun/Xwindows, and primegen. Also check
EBI's
list of primer design programs.
More information about primer design can be found at:
Restriction
Maps and PCR primer design, a course at NYU.
PCR
primer analysis, a course from U. Kentucky.
How do I convert peptide sequences from 1-letter to 3-letter amino
acid codes?
Reformat,
which converts other sequence formats into GCG format, can do this.
You would run it with the '-ONEintothree' option, and your input
sequence file can be either GCG format or any of the other formats
that Reformat accepts. Note that reformat will write over your
input sequence file, so save a copy if you want to preserve the
original!
Sample session:
helix% more jc5122.pir2
P1;JC5122 - superoxide dismutase (EC 1.15.1.1) (Mn) |