Hi,

if you are familiar with R, you could try one of the approaches suggested here:

https://stackoverflow.com/questions/6529675/how-to-get-pair-wise-sequence-similarity-score-for-1000-proteins

Hi,

if you are familiar with R, you could try one of the approaches suggested here:

https://stackoverflow.com/questions/6529675/how-to-get-pair-wise-sequence-similarity-score-for-1000-proteins

There are several software tools both online based (EMBL -clustal w, EXpasy, T-COFFEE etc.) and app based (MEGA, Seaview where you can perform multiple sequence allignment for DNA, RNA or Protein. For heatmap, you may upload the MSA file in SigniSite.

@Daniel Fischer, thank you very much,

very useful answer for me. Yes, familiar with R :-)

Needleall with two identical files?

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

@Julia Varga, great solution, thank you for the tip, finally I found also user friendly web version of Needleall (http://www.bioinformatics.nl/cgi-bin/emboss/needleall)

we can use BioEDIT and MEGA (https://www.megasoftware.net/) software for alignement and also, can get the identity values to make heatmap identity plot.

Hmm...Martin let me know if any of these methods worked out for you. It might answer a similar question for me.

@Noble Iheukwumere Egekwu,

Needleall (http://www.bioinformatics.nl/cgi-bin/emboss/needleall) works pretty well for me. You can change many parameters and select between many output formats :-)

Thanks @Martin. I will look at this

You can download and install BLAST as a standalone package, with all standard server-side modules avaiable (at least, you used to be able to 15+ years ago) After this, you can run it as many times as you want. I remember using bl2seq from the command line to automatically grade student answers when they had to read a sequence from a gel. I had it passing strings back and forth with Python. It is much faster locally, too.