Bioinformatics for Nucleotide Sequence Analysis
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BIOINFORMATICS FOR NUCLEOTIDE
SEQUENCE ANALYSIS
BIOC 2112125-05-2015
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Home page of NCBI
http://www.ncbi.nlm.nih.gov/
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What can we do with NCBI ?
To find similar sequences – Sequence AlignmentTo find the relatedness of a gene or protein (do they have a common ancestor?)To study mutationsPrimer designing
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WHAT IS BLAST ? Basic Local Alignment Search Tool A method for rapid searching of nucleotide
and protein databases Offers both sensitivity and speed Fastest and most frequently used sequence
alignment tool
Align 2 or more sequencesPrimer blast
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BLAST ACCESS NCBI BLAST http://www.ncbi.nlm.nih.gov/BLAST/ Canadian Bioinformatics Resource BLAST http://cbr-rbc.nrc-cnrc.gc.ca/blast/ European Bioinformatics Institute BLAST http://www.ebi.ac.uk/blastall/ http://www.ebi.ac.uk/blast2/
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BLAST - PROGRAMS Blastp - Compares an amino acid query sequence against a
protein sequence database.
Blastn - Compares a nucleotide query sequence against a nucleotide sequence database.
Blastx - Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
Tblastn - Compares a protein query sequence against a nucleotide sequence database.
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Accession Number - NM_008862
TCGAAATAACGCGTGTTCTCAACGCGGTCGCGCAGATGCCTTTGCTCATC AGATGCGACCGCAACCACGTCCGCCGCCTTGTTCGCCGTCCCCGTGCCTC AACCACCACCACGGTGTCGTCTTCCCCGAACGCGTCCCGGTCAGCCAGCC TCCACGCGCCGCGCGCGCGGAGTGCCCATTCGGGCCGCAGCTGCGACGGT GCCGCTCAGATTCTGTGTGGCAGGCGCGTGTTGGAGTCTAAA
Q1 : Find the protein coded by the following nucleotide sequence.
http://www.ncbi.nlm.nih.gov/
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BLAST StatisticsThe Score and the E-value (E) are particularly helpful in making interpretations.
Score - a good measure of the quality of an alignment.E-value - expectation value is a good measure of the
significance of the alignment.
The E-value is the number of different alignments, with scoresequivalent to or better than S, that are expected to occur in a database search by chance.
Significant the alignmentE value
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Toll-like receptor 3 - human - NM_003265 - mouse - NM_126166 - zebra fish - NM_001013269
Q2 : Find the relatedness of the following receptors.
http://www.ncbi.nlm.nih.gov/
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Crassostrea gigas heat shock protein70
Q3 : Design primers for the following gene.
http://www.ncbi.nlm.nih.gov/
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Q4 : Determine the fragment size of the following PCR product.
TubA1 U12589Alpha tubulin gene of Forward 5’ GGAAACGCCTGCTGGGAGReverse 5’ AACAGTTGGAGGCTGATAAT
http://www.ncbi.nlm.nih.gov/
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CONCLUSIONS BLAST is one of the most important program in
bioinformatics (maybe all of biology) BLAST is based on sound statistical principles
(key to its speed and sensitivity) A basic understanding of its principles is key for
using/interpreting BLAST output
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