databases for mafft-homologs
This repository contains the databases (and sub-method) needed for some sub-aligner in PASTA
See https://github.com/smirarab/pasta/ for the most up to date version of PASTA and instructions
How to install:
Follow the instructions in the README.md within PASTA for downloading PASTA and the appropriate sate-tools (linux or mac)
Change directory to sate-tools-linux (or sate-tools-mac)
Download this repository git clone https://github.com/kodicollins/pasta-databases
Continue with the installation instructions within PASTA
The databases are for use in MAFFT-Homologs Katoh, K. and Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780.
See https://mafft.cbrc.jp/alignment/software/manual/mafft-homologs2.1.html for more information about MAFFT-Homologs
The databases within this repository are SWISS-PROT
Bairoch, A., & Apweiler, R. (2000).
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.
Nucleic Acids Research, 28(1), 45–48.
See http://www.uniprot.org/ for the most up to date version of SWISS-PROT
The sub-method used by MAFFT-Homologs is BLASTALL Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
See http://nebc.nerc.ac.uk/bioinformatics/documentation/blast/blastall.html for more information about BLASTALL
If you would like to use anoter database with MAFFT-Homologs inside of PASTA, you will need to add the datasets to this folder, and you will need to edit the homologs file within sate-tools-linux (or sate-tools-mac) and change the localdb accordingly
localdb = "$CONTRALIGN_DIR/pasta-databases/swissprot" <- this line specifically
the last part ('swissprot') should be the beginning of the database files you would mafft-homologs to use.
Note: If you decide to add these databases after installing PASTA, you can either reinstall PASTA or just untar the files manually.