A tool to align two assembled sequences

Question

[User000]

Hello,

I have two assembled sequences and I would like to compare them. I am interested to get to know the similarity % between them, how many bp's were aligned, number of gaps, the score bit, where the alignment starts and finishes. I used blastn, but the since the alignment is local it gives results as blocks. I was wondering what would you suggest me to use to get an overall result of an entire alignment?

Answer 1

[samuelmiver]

Take a look to the web tools provided by the EMBL-EBI. Try with the pairwise global alignment tools:

http://www.ebi.ac.uk/Tools/psa/

I have tried with two very big sequences and Needle run without problems

In case you were needing a multiple sequence alignment:

http://www.ebi.ac.uk/Tools/msa/

It has a brief description and suggests the most suitable scenario for each one of the tools. For all of them you only need to paste or upload the sequences in a supported format (FASTA for instance).

[User000]

Thank you. I have already tried muscle and emboss, however apart the alignment itself, I need to get the statistics..

[michael.ante]

Why don't you use emboss' Needleman-Wunsch implementation "needle"?

In its report you'll find:

# Length: 15
# Identity:      11/15 (73.3%)
# Similarity:    11/15 (73.3%)
# Gaps:           3/15 (20.0%)
# Score: 41.0

[User000]

hi,

I have tried to use emboss matcher (needle dies, because my sequences are too big). But it takes only 1 per 1 sequence at a time and prints me output. Do you know if there is a way to run a batch mode?

[samuelmiver]

Try with the pairwise global alignment tools:

http://www.ebi.ac.uk/Tools/psa/

I have tried with two very big sequences and Needle run without problems

[samuelmiver]

Remember to upvote when you get a good/useful answer in order to help people with same problem find the best solution.

[samuelmiver]

With statistics do you mean the score? It will change depending the algorithm as it is computed in different ways. What score do you need?