== Review Articles ==

Review article by [http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030123 Cedric Notredame][[br]]
[http://www.genomeweb.com/alignment-algorithms-0 Genome Technology article] by Fran and George

== Start with sequences from a database ==

Useful alignment algorithms - available on the web, for desktop computers, and for Linux systems

[http://www.drive5.com/muscle/ muscle]   '''muscle -in MySeqs.fa -out MySeqs.aligned.fa''' [[BR]]

[http://www.tcoffee.org/ t_coffee]    '''t_coffee MySeqs.fa''' [will create MySeqs.aln] [[BR]]

[http://mafft.cbrc.jp/alignment/software/ mafft]  '''mafft --auto MySeqs.fa > MySeqs.aligned.fa''' [[BR]]

The output from these programs can then be visualized in [http://www.clustal.org/ ClustalX] or [http://www.jalview.org/download Jalview].

Our favorite method is to use the T-COFFEE suite (more specifically, M-Coffee) to run multiple alignment methods and then create a consensus alignment, a sort of a meta-alignment. This can be done with a single command like


{{{
t_coffee my_proteins.fa -method=t_coffee_msa,mafft_msa,probcons_msa,muscle_msa -output=fasta_aln
}}}


The final consensus alignment will appear in the file my_proteins.fasta_aln, which can them be viewed in ClustalX.


== Start with genome coordinates ==

This method will detail how to extract a slice of a pre-computed genome-genome alignment from the UCSC Genome Browser.

* Select region in UCSC Genome Browser (ex: chr19:100,000-100,100 in human hg19 assembly)
* Click on Tools > Table Browser
* In the Table Browser, make these selections:
  * group => Comparative Genomics
  * table => Multiz Align
  * region => position (which should show the region you began with in the genome browser)
  * output format => maf
* Click "get output" button
* Copy/paste or save MAF file (ex: MyRegion.maf)
* Few programs understand MAF format, so you may need to convert the alignment to a format like fasta.  
    * By selecting the "-" strand, the program will reverse-complement the alignment.  
    * 'refGenome' should be the UCSC Bioinformatics assembly name (like hg19 or mm9).

{{{
# USAGE: maf_alignment_to_fasta.pl mafFile refGenome regionName strand[+-] > regionName.fa
Sample command:
  /nfs/BaRC_Public/BaRC_code/Perl/maf_alignment_to_fasta/maf_alignment_to_fasta.pl MyRegion.maf hg19 myRegion + > Gata4.NEW.fa
}}}