Nov 12, 2023
Multiple Sequence Alignment
- 1University of California, San Diego
Protocol Citation: Leonardo A Parra-Rivas 2023. Multiple Sequence Alignment. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2lyj14wlx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: November 12, 2023
Last Modified: November 12, 2023
Protocol Integer ID: 90823
Abstract
Multiple Sequence Alignment
Protein sequences were retrieved from Uniprot or NCBI via Jalview’s sequence fetcher Jalview
(RRID:SCR_006459)(https://www.jalview.org/help/html/features/seqfetch.html).
Then, the sequences were aligned with the
Clustal Omega Webserver [(RRID:SCR_001591) http://www.ebi.ac.uk/Tools/msa/clustalo/]
with default parameters.
For the α-synuclein alignment human (uniprot OP37840), chimpanzee (uniprot P61145), baboons
(uniprot A0A2I3N0Z9), marmoset (uniprot F7GY62), rat (uniprot P37377), mouse (uniprot O55042), rabbit (uniprot G1U0V2),
cow (uniprot Q3T0G8), bat (uniprot A0A6J2L5S3), shrew (uniprot J7H0X3),
armadillo (NCBI XP_004480597), elephant (uniprot G3T7Z3), tenrec (NCBI
XP_004703317.1), chicken (uniprot Q9I9H1), zebra finch (uniprot Q4JHT6), frog
(uniprot Q7SZ02), and fish (uniprot
A0A090D865) sequences were used.