need to know the AA residue and what has changed from the original protein seq.
If you are familier with python you can use the biopython library which has a function exactly for this.
http://biopython.org/wiki/Seq#Translation
Otherwise, you can have a look at the EBI website: http://www.ebi.ac.uk/Tools/st/
P.S.: If your sequences come from mitochondrial genomes, you have to take care of corresponding genetic code.
If you have the gene code (e.g. genebank code) you can use the sequence viewer available at http://www.ncbi.nlm.nih.gov/projects/sviewer/ this web tool is able to translate the original gene in the corresponding protein. Moreover if you want establish the effect of mutations in your protein by using the above mentioned tool you can do it...
Happy sequence analysis
i agree with Gaurav. the Bio Edit and Unipro UGENE is a good program too.
Maybe the fasta programs http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml
You can convert a DNA sequence to RNA residues using the free ExPASy web tool (http://web.expasy.org/translate/) and then align two protein sequences using protein BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=blasttab)
Hope this helps!
Hi Rhiannon,
The SABC at Murdoch University has a licensed version of CLC Genomics Workbench that could be used for this purpose. I understand there are plans to obtain appropriate licenses for Geneious as well. In addition to the programmes and websites suggested above there is one I use frequently "Translate a sequence" - it does just that in all frames with the nucleotide sequences below each amino acid. Also, ORF Finder from NCBI tools will do a similar thing. You can let me know how you go with any of these.
you can translate ur sequence using http://web.expasy.org/translate/
and choose the longest oRF follow the link and blast to see what type of protein it is.
After that you can download the desired relevant proteins and clustalw alignment can be done online or by using softwares like mega 5, DNA star, et
@RM
If you are serious, please remember that all good things are not FREE. You have to pay for accuracy, comprehensiveness, ease of operation, and most importantly-- the algorithm embedded in the tool.....
Therefore, I would suggest you to try
1. SciFinder of CAS
2. CLC
If you can share the sequence, I can help you in ""translation and comparing it with others" using some paid softwares as 1 and 2
Like Ali, I also use Bioedit for that task. Quite easy tbh, open your FASTA file with your sequence, CTRL+T to translate and if the sequences are already aligned,i.e one wildtype and you're mutant, then you can just compare them straight over.
And just to reply to the other comment, all good things SHOULD be free! And fortunately most things are when you work with sequences..
I use MEGA 7 and now MEGA X. It works for me if dataset are not too big.
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