Nile University, Bioinformatics Group. Cluster Computer For Bioinformatics Applications. Hisham Adel 2008. Done By:. Hisham Adel Hassan. Supervised by: Dr. Mohamed Aboualhouda. Points. Introduction. Cluster and Supercomputers. Cluster Types and Advantages. Our Cluster.
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Cluster Computer For Bioinformatics Applications
Hisham Adel Hassan.
Dr. Mohamed Aboualhouda
Communication : Switch 5-Port 10/100Mbps.
Processor and Ram:
Duo core Processor 1.86 GHZ.
Ram 512 MB
Used to :
1-Compare between sequences.
if we have two sequences A A A C G A
A A T G A
Let match=1, gap=-1 , miss-match=0.
they can be aligned as:
1- A A A C G A
| | | | | | Score=3
A A T _ G A
2- A A A C _ G A
| | | | | | | Score=1
A A _ _ T G A
(Basic Local Alignment Search Tool)
(High scoring pairs)
BLASTN -Compares a nucleotide query sequence against a nucleotide sequence
BLASTP- Compares an amino acid query sequence against a protein sequence
TBLASTN- Compares a protein query sequence against a nucleotide sequence
BLASTX- Compares nucleotide query sequence against a protein sequence database.
Nucleotide sequence database “formatdb -i DATABASE -p F “.
Protein sequence database “formatdb -i DATABASE -p T “.
“blastall -p BLAST Search Type -d DATABASE -i QUERY FILE -o out . Txt”
Average of running 1000 Query, 1000 times.
Compare between sequences