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Bioinformatics Shared Resources
Sanford Burnham Prebys Medical Discovery Institute
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i-have-i-want
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I HAVE, I WANT TO...
Quick answers to straightforward bioinformatics questions.
What I have:
What I want to Do:
Single DNA sequence
translate it:
Expasy
design primers/probes: use
Oligo
on PC/Mac
mask repetitive sequences
:
RepeatMasker
find open reading frames (ORFs):
ORFfinder@NCBI
find out what it is:
BLAST
find its genomic location:
Ensembl
Multiple DNA sequences
assemble into contigs: use phrap on emu (ex: > phrap dna_fasta_file.fa)
compare using a dotplot: use dotter on emu (ex: >dotter dna_fasta_file1.fa dna_fasta_file2.fa)
Single protein sequence
find
out what it is:
BLAST
Multiple protein sequences
align them:
TCoffee