I have a nucleotide sequence and when making a BLAST search for this sequence, I found the identity % to other sequences; However, I would like to add also the % of amino acid identity. How is it possible to find the % similarity of the aa? (when performing a blast of the protein sequence, if gives the same %).
Thank you
Dear Faten
you can you 2 approaches:
1) Translate your protein in aminoacid sequence (eg using ExPASy - Translate tool ) and afterward perform the BLAST with the aminoacid sequence ad input
2) Download all the Dna sequences coming from blast, translate them and perform a CLUSTALW alignment
NPS@ : CLUSTALW multiple alignment (ibcp.fr)
Clustal Omega < Multiple Sequence Alignment < EMBL-EBI
If you are intested to see an overview of simple online tools free avialable for DNA and protein analisys you can see those 2 video
https://www.blogger.com/video.g?token=AD6v5dzuvzGmtB3Spee0N6qDyoJEshv3gVqU_I211PMbwaZIYnrEJccR6fGRXiYCG5z6jSCM5Id3JcK7BMUgC52_YRj8oXFux5tFj-yLi6GtvtAcPMHXo9YvX5Yv_679lq2pXOjV2JM9
https://www.blogger.com/video.g?token=AD6v5dyPGWsbPCAGPM4bhC7qrFmUL9TIfeArxzSqZ-ao_K6iC3z597YtqkSB2QIvBIxy9TVU52O9By7lhSuO-TFmnmd1-xRgRxnhW6uEon8lV-Lk-zMV2mZq1MT0o4gwaT38-wIRIIY
available on my blog, ProteoCool
ciao
MAnuele
hello Manuele Martinelli , thanks for your reply.
Well I have done (1) but the % given is the same as the % given when I blast the nt. I thought it shouldn't be the same but slightly different.
and also I have done (2), but the same as (1).
Thanks also for your videos, will check them out.
Dear Faten,
Have you tried these program:
NCBI BLAST+ https://www.ebi.ac.uk/Tools/sss/ncbiblast/
The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your novel sequence.
or
FASTA [protein] https://www.ebi.ac.uk/Tools/sss/fasta/
This tool provides sequence similarity searching against protein databases using the FASTA suite of programs. FASTA provides a heuristic search with a protein query. FASTX and FASTY translate a DNA query. Optimal searches are available with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).
Dear Faten
is seems quite strange that % of similarity is the same in DNA and protein sequence. It is possible if it is equal to 100% or very close to it, but otherwise the fact that the same aminoacid can be codified by different DNA codon have to induce differences in terms of % beetween the 2 alligments:
eg is possible that 2 sequeunces has
Dear all,
I wanted to add that I found out that we can compare sequences with MEGA and BioEdit software. For nucleotide, we can perform pairwise distance on MEGA and we can get the similarity between isolates. For amino acid, when retrieving sequences from Genbank make sure that they start with the start codon that codes for methionine (in NCBI, for the sequence we need to use, we should look for ''CDS'' that indicates where the ORF starts). Then, we can compare using pairwise distance also.
Hope this helps.
Neither the % identity nor the % similarity need to be the same for nucleotide and protein sequences. Due to the degeneracy of the genetic code, different nucleotide sequences can encode the same amino acid sequence. The % similarity depends on the substitution matrix used, and this should be chosen according to the degree of relatedness of the sequences to be aligned.
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