Sequence Alignments HEXA

Sequence Alignments

Sequence Searches:

• FASTA

/bin/fasta36 seq.fasta /data/blast/nr/nr > fasta_out.txt

• BLAST

blastall -p blastp -d /data/blast/nr/nr -i mult_seq.fasta > blast_out.txt

• PSIBLAST

blastpgn -i seq.fasta -j <#iterations> -h <e-value threshold> -d /data/blast/nr/nr > psiblast_out.txt

• HHSearch

For the HHSearch tool we used the online server for HHSearch.

Multiple Alignments

• Cobalt

Download Cobalt from ftp://ftp.ncbi.nlm.nih.gov/pub/cobalt/executables/2.0.1/ (ncbi-cobalt-2.0.1-x64-linux.tar) Uncompress the archive file with tar xfz ncbi-cobalt-2.0.1-x64-linux.tar and change directory to the uncompressed cobalt directoy. Call: ./cobalt -i mult_seq.fasta -norps T > cobalt_out.aln

• ClustalW

clustal -infile=mult_seq.fasta > clustalW_out.aln

• Muscle

muscle -in mult_seq.fasta -out muscle_out.aln -clw

• T-Coffee

t_coffee -seq mult_seq.fasta

• T-Coffee (3D)

t_coffee -seq mult_seq.fasta -mode expresso