Using Blast online
Blast is one of the most used bioinformatics tools ever written. It allows to find similaroties between sequences of proteins or nucleotides, at a reasonable speed.!
Its ancestor, the fasta suite (like the format) used an algorithm clled smith-waterman. While very accurate, was very slow.
Blast is available opnline on the ncbi website at the following address https://blast.ncbi.nlm.nih.gov/Blast.cgi
Let us try it out!
Your first blast
go on the blast ncbi website and select protein blast
Copy and paste the following protein sequence
>a_protein
MKWVTLISFIFLFSSATSRNLQRFARDAEHKSEIAHRYNDLKEETFKAVAMITFAQYLQR
CSYEGLSKLVKDVVDLAQKCVANEDAPECSKPLPSIILDEICQVEKLRDSYGAMADCCSK
ADPERNECFLSFKVSQPDFVQPYQRPASDVICQEYQDNRVSFLGHFIYSVARRHPFLYAP
AILSFAVDFEHALQSCCKESDVGACLDTKEIVMREKAKGVSVKQQYFCGILKQFGDRVFQ
ARQLIYLSQKYPKAPFSEVSKFVHDSIGVHKECCEGDMVECMDDMARMMSNLCSQQDVFS
GKIKDCCEKPIVERSQCIMEAEFDEKPADLPSLVEKYIEDKEVCKSFEAGHDAFMAEFVY
EYSRRHPEFSIQLIMRIAKGYESLLEKCCKTDNPAECYANAQEQLNQHIKETQDVVKTNC
DLLHDHGEADFLKSILIRYTKKMPQVPTDLLLETGKKMTTIGTKCCQLGEDRRMACSEGY
LSIVIHDTCRKQETTPINDNVSQCCSQLYANRRPCFTAMGVDTKYVPPPFNPDMFSFDEK
LCSAPAEEREVGQMKLLINLIKRKPQMTEEQIKTIADGFTAMVDKCCKQSDINTCFGEEG
ANLIVQSRATLGIGA
into the "enter query sequence" form
and click "Blast" (you may have to scroll down a bit)
then wait for your results. Once the results have loaded, scroll down to the first hit.
Question
From which organism is our protein? What is it?
Note
Sometyimes, two hits have an identical score. In that case, be careful with the interpretation.
Restrict the search parameters
Let us imagine we'd like to compare our query to only human proteins. We can select an organism to restrict our search.
Question
What is the percentage identidy between the chicken and human albumin?
Question
Here is an unknown protein. From which organism and which function does it have?
MVLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
AKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTP
AVHASLDKFLANVSTVLTSKYR