Sequence Alignments HEXA

From Bioinformatikpedia
Revision as of 10:07, 23 May 2011 by Link (talk | contribs) (Sequence Alignments)

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.


Result Statistics

We wrote a script, which shows the distribution of the E-Value and the Identity and also the different aligned sequences. To analyse the overlap between the different methods, we drew a Venn diagram (with http://bioinfogp.cnb.csic.es/tools/venny/index.html). We compared the BLAST, FASTA and Psiblast method (PSIBLAST with 3 and 5 runs and E-Value cutoff from 10E-6)

Comparison ali.png

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

clustalw -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