I would like to run multiple alignments for proteins in ~20 mammalian species. At the moment, I am retrieving the sequences manually from Ensembl and entering them in ClustalW2. Is there a more efficient way to retrieve and align the sequences? Any help is appreciated.
Thanks, Eric
2 answers
If you only need to retrieve existing alignments from Ensembl, you can use the data dumps or the Perl API. If you need to incorporate extra sequences to the alignment, you can do it with PAGAN.
•
written
by
2184687-1231-83-
The easiest way is to download all the FASTA sequences from the species from the FTP server at ENSEMBL. Then you could store them in a python dictionary or a perl hash... (etc) and just feed the alignment programme with the sequences you want to align in each run. Fast & efficient. I do this all the time with python + mafft (or prank-F) but can be implemented with other programming languages and/or alignment programmes.
Log in to answer this question.
-
Generate nucleotide multiple sequence alignment from protein alignment?
written by molly77 •
-
Retrieve many FASTA of the same gene from NCBI..
written by uwardgma •
-
Batch-retrieving protein domain sequences from InterPro
written by mucmvsthlm •
-
Ensembl Multiple Genome alignments do not yield the same as pairwise alignments
written by except.for.me.and.my.monkey •
-
Downloading All Gene Families From Mammalian Species In Ensembl
written by Marki •
-
Deleting Stop Codons
written by Eric •
-
How To Retrieve Upstream Sequences Of A Single Gene From Multiple Bacterial Species?
written by Magdalena •
-
Single Position Highlight In Multiple Sequence Alignment
written by Kamila001
-
Align Multikb Contigs Of A Mammalian Genome Against List Of Mammalian Genome Assemblies
written by Ahdf-Lell-Kocks •
-
Retrieving Sequence From Noncoding Rna
written by Eric •
An aside: If you're aligning proteins, use Clustal Omega instead of ClustalW2. It's faster and produces alignments of higher quality