BLAST or ClustalW?

Dear Balder,

Thanks for reply.

I have Bioedit and Mega softwares , is it possible to using these softwares to calculate % of similarity and identity ?

Best Regards

Oumed

Dear Oumed,

You can perform BLAST search to find out similarity/identity of your query sequence to database sequences through MEGA software. It has an inbuilt module which can directly access BLAST. See this link for a tutorial:

http://www.virology.wisc.edu/acp/tutorials/MEGA.pdf

Depending on the number of sequences, it could be of use to install a local version of BLAST. This would be the preferred route of course, only if you have a large number of sequences.

For a small number of query sequences simply run BLAST on the NCBI servers through this website:

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Dear Quiroga,

Thanks alot.

However I want to compare my own sequences and to find out how similar they are to each other! please see page 407 in the attached file.

1) Go to nucleotide blast or protein blast at http://blast.ncbi.nlm.nih.gov/Blast.cgi

2) Look for "Align two or more sequences" which does "Enter one or more queries in the top text box and one or more subject sequences in the lower text box. Then use the BLAST button at the bottom of the page to align your sequences."

That should be what you are looking for.

You can find this kind of pairwise table with CLUSTALW.

After aligning all sequences you can find different results generated by clustalw. One of them will be pairwise comparison and scores of your aligned sequences.

Hope this works!

Thanks alot.

In BLAST (NCBI) you have this option when you can compere your own 2 sequence, in clustalw you can align more then 2 sequences in the same time, but in the summary table you can't find the similarity and identity of sequences only score for alignment. So the best way is use blast and compere the pairs of sequences.

Dear Oumed,

Blast and aligning are the best way to inform yourself about similarities. However, you may also want to know the percentage of conservation. If for example you want to determine any functional properties/implication of a mutation. Such an analysis can be performed on http://bental.tau.ac.il/new_ConSurfDB/

Good luck,

René

It is best to get these figures from a multiple sequence alignment. You can use SIAS at http://imed.med.ucm.es/Tools/sias.html

Dear Pedro,

I appreciate to tell me source of SIAS ? how to convert the SIAS similarity to text to copy it to word or excel?

Dear Farhan,

How to convert CLUSTALW similarity results to text for copying to another document such as word, excel, etc..?

SIAS results are html tabulated. If you select them you can copy them in excel.

Dear Dr Perdro,

I tried it is very hard to select the sequences and copy them to excel and then to word as in word the table will lose the format and help is appreciated.

Dear Oumed

As I remember, you can download the text file of as output.

If you cannot download them as text file just copy those files , paste them in a word file and save it.

Hope it works

You need "percent Identity Matrix" right ? Just copy paste that.

If it looses format. use any scripting language to organize it in an excel or tabulated format.

Does sequence similarity information conform with phylogram information on the same sequences? I mean if 2 sequences have 90% nucleotide or aa similarity are also placed in the same clade when phylogenetic analysis were done?

yes. In Phylogenetic trees, high sequence identity sequences are clustered together or closely clustered. If the similarity is low then the sequences will be far apart from each other in a phylogram.!

Thanks alot.

I also appreciate to tell me how to find stop codon in a sequence consist of multiple genes ;Vp2, Vp4 and Vp5 Genes?

How to remove Gene Vp2 from a sequence of multiple genes?

well. if you want to find a stop codon in a nucleotide sequence of gene. you can use different tools. One example is :

http://web.expasy.org/translate/

Dear sirs ,

Thanks alot for the answers