Bioinformatics Basic Usage (NASC)

Phenotyping Bioinformatics Practical

Sequence Comparison

A basic introduction to BLAST as a tool for sequence comparison,

We will give you a brief description of the concepts behind sequence similarity comparisons and the use of BLAST as a tool.

IMPORTANT: READ ALL OF THE INSTRUCTIONS

Protocol for gene 1:

Go to The blast server at NASC
DO NOT change any of the choices.
Read all of the text
Note the differences between the blast programs

Now - put your first DNA sequence into the appropriate box and perform a blast search

Sequence 1
GTCAGGAGGAGTAGGAGATGAAAGAGAGACAACGTTGGAGTGGTGAAGAAGATGCATTGT TACGTGCTTACGTTAGACAGTTCGGTCCGAGAGAATGGCATCTTGTGTCTGAGCGTATGA ACAAACCTTTGAACCGTGACGCCAAGTCTTGTTTAGAGAGATGGAAGAATTATCTTAAGC CAGGGATCAAGAAAGGGTCTTTGACAGAGGAAGAGCAGAGGCTTGTGATCCGTCTTCAGG

Wait for a match to appear

What is the chromosome position of the top match ?
Type it here:

What is its 'E-value'? :

What is the chromosome position of the next highest match ?
Type it here:

What is its 'E-value'? :

Use the dropdown for the best match to see the ContigView (context).

What is the title of the gene ? :

Section Two

So what is an E-value and what does Blast do ?
Please find some answers here

Please answer the following questions (briefly) using the help files at any of the links above (or Google):

What is blastp, how does it differ to blastn ?

What is blastX ?

What is TblastX ?

Now perform the same procedure with these sequences:

Sequence 2
TCCTCCAAGTTGAATCATTTTTTGTATGATGCCAGAATGGGCCTCCCCAGTACCGTAGCA GAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGT TCCGTTCCAAGTGGGATGATATGCTTTTGTATTCTTCTACTCTCGAGCGTTGCAAGGACA CGGGCACTATGGTTGTGCAATGGGTGCGAAAGGTCGCTACTTGTTTCTCTTTTTTCTTCG
Sequence 3
CGTTAAGCCATTGTTTGAGGCAATGGGAGAGCAGAACAAAGTGGTACAATCTGGAGCTTC AATGTGTATGGCTAGGATGGTTGAATCAGCTGCTAGTCCTCCAGTTACTTCTTTCCAAAA GCTTTGCCCTAGAATTTGCAAGCTATTGAGCAATTCCAGTTTCCTTGCTAAGGCTTCCCT TTTGCCAGTTGTTTCAAGTCTCTCTCAGGTTTGCCCAGAATCCTTATAATCTCCTCCTTG
Sequence 4
TTTACATGCTATTAAAGGTTGTGCATGAAAATTTCTTTTGCTGTTCGTATTTGTTTTACA CCTAAACGAAGATTTTTACTTAAAATTAAAGAAAAAAAATTATACTAATTTTAGTTACGT TGCGTATTGCTAGCTTCTCCTATAAAGTCGTTCAAATTTTTACACGCTTGTCTTCTTGTA AATGAATTCGTGGGAAAATTTTGTATGAACACGTGTTTCTGTGTTGGAACAGTTCTTTAT
Sequence 5
GAGAAGTCTGTTGTTGAGACTCAGCTTATAGCTCATGATAAAGAGGTTCATGACATTGCT TGGGGAGAAGCTAGGGTTTTCGCATCAGTCTCTGCTGATGGATCCGTTAGGATCTTTGAT TTACGTGATAAGGAACATTCTACAATCATTTACGAGAGTCCTCAGCCTGATACGCCTTTG TTAAGACTTGCTTGGAACAAACAAGATCTTAGATATATGGCTACGATTTTGATGGATTCT
Sequence 6
GACCAAACGGCGATGAGGAGGAACAATCTGGATCTGACTCTTGAACCCATTTACAATTAC CTTGGCTGTTACGCCGCTTGAATAGACTACATCGATCTATATCAATCTCTTTAAAATAAT ATAAGATCGATCCTCTACTCATGATCTATATTAAACACCGGTTAATTAATATATTTTTGG TATGTCCTTATATCATATCAACATGATCAAGCCTTTTTCCAATTCAATATATCTTGTATT
Sequence 7
TAATGCACGCTATGTGGAAACCGCAAAAGTTCAAGGCGATATATCTACTAGCGACCATAT ATGTACTAACGCTAACGCTACCATCCGCGTCTGCGGTTTATTGGGCGTTTGGCGATAAGC TACTAACTCATTCCAATGCGCTCTCTCTTCTCCCTAAGACTGGTTTTAGAGATACCGCAG TGATCCTCATGCTCATTCATCAATTTATAACGTTCGGATTCGCGTCTACACCGTTATATT