Methods and Websites

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Editing help (since our help is not yet functional)

Websites with useful information or software

  • RCSB Protein Database: PDB
  • Structural Classification of Proteins: SCOP
  • Structural Comparison of Proteins: Dali, CE
  • Multiple Structure Alignment: CEMC
  • Clusters of Orthologous groups: COG
  • Protein-protein interaction:

STRING: a database of predicted functional associations between proteins
PII: The MIPS Mammalian Protein-Protein Interaction Database
iHOP (Information Hyperlinked over Proteins). Protein association network built by literature mining

  • A program to score residue conservation in a multiple sequence alignment Scorecons
  • Computed atlas of surface topography of proteins CASTp
  • Webserver that converts sequence identifiers into species names.

The website lets you change the sequence identifiers to organism taxonomies. You need to upload the original FASTA file with all sequences and a second file (e.g. the Newick tree file, but could be any other (text) format). The result you get back from the web page will have replaced identifiers by taxonomies where possible in the second file.

  • Reactome a curated knowledgebase of biological pathways

Additional tips for Deep Evolutionary Analysis

Tools/Papers for function analysis

CD/DVD software, basic how to use

blast clustalx muscle seaview phylip-3.36 treeview rasmol pymol


Call up a command prompt (accessories), it should be H: (your student directory)

D:\blast\bin\blastall -p blastp -d D:\blast\databases\nr -i yourfile.fasta -o usefuloutputname.blast

NOTE: D is the letter of your CD-ROM.

NOTE: You need to specify an input file (i.e. on H:\ your student directory)

NOTE: You need to be able to write to an output directory i.e. H:\ (this is your student directory.

i.e. D:\blast\blastall -p blastp -d D:\blast\databases\nr -i H:\yourfile.fasta -o H:\usefuloutputname.blast

-p the blast program to use: blastp, blastn

-d the database to use:

On the DVD we provide a non-redundant sequence data base (nr), sequences from the proteins in the PDB (pdb) and a selected subset of the RefSeq database (fungi invertebrate plant protozoa vertebrate_mammalian vertebrate_other). You can search several databases by putting quotes around them: -d "vertebrate_mammalian vertebrate_other"

-i input, query sequence (in FastaFormat)

-o output file to write blast results to.


Psi-blast is very similar, but you need to use "blastpgp" and be aware of -j and -h options. Also remember that psi-blast will generally be slower because it has to do normal blast first, and then build profiles and do later rounds of searching with the profiles.

E:\blast\blastpgp -d e:\blast\databases\nr -i yourfile.fasta -o usefuloutputname.blast -j 3 -h 0.000001

-j maximum number of rounds to do (it will stop earlier, once the searches don't find more matches)

-h significance level cut-off

The documentation with all possible options is on the CD/DVD under blastdoc.

Obtaining FastaFormat files of the sequences found with blast:

Call up a command prompt.

E:\blast\bin\fastacmd -d E:\blast\databases\nr -i filewith_img_numbers -o H:\newsequences.fasta

-i the input file should be a line-by-line listing of the "accession numbers" from the same img database you used in the blast search.




ExtractIDs.doc shows a fast, painless way to prepare the input file from your blast result.

The complete fastacmd document is here.


Click on the clustalx.exe icon in the clustal folder. Load sequences (you can use "browse" to go to your student area files) in FastaFormat.

Select options from the various clustal menu items.

Alignment output defaults to .aln (which can be loaded back into clustal later); select phylip output format also (.phy) for phylip analysis.

Remember to change the output format options from branch to NODE before bootstrapping in clustal. If not, you will not be able to see the reliability of the branches in treeview (shown with the internal edge labels).


Click on the icon for the appropriate program in the phylip exe folder. Type in the input file name eg H:BIOL3004mydata.phy. Most phylip programs take .phy input files; neighbor takes a distance matrix produced by protdist, dnadist or similar.

For more instructions on how to use phylip to construct a phylogenetic tree, see the Phylogenetic tree page

Complete phylip documentation is also on the DVD: click on the phylip.html document in the phylip folder, it has links to documentation for specific programs. Or, on the web, you can find it here.


Click on treev32.exe in the Treeview folder. The input file should be a tree in NewHampshire format.

From clustal: filename.phb

From phylip: outtree (renamed appropriately)


PyMOL is a powerful molecular visualiser. Click on PyMOL.exe in the Pymol folder. The input is a protein structure file, such as a PDB file.

The best place to learn about PyMOL is the PyMOL wiki:

Some brief notes on using PyMOL to do structural alignment: PyMOL alignment

How to use APBS within PyMOL is described here.

How to visualise surface topographies computed by CASTp is described here

More information on PyMOL will be uploaded soon. The PyMOL Reference Manual and the PyMOL User Manual may also be useful.

a brief PyMOL tutorial


Click on rasmol.exe in the Rasmol folder. The input is a protein structure file, such as a PDB file.

Perhaps useful links



'png', 'gif', 'jpg', 'jpeg', 'pdf', 'doc', 'txt', 'aln', 'dnd', 'ppt'


--ThomasHuber 13:43, 24 April 2007 (EST)