Reference APSES domains (reference species)
- Multi FASTA file of all APSES domains in fungal proteins.
Generating this file turned out to be much more difficult than anticipated:
One feature I wanted this file to have is headers that identify the yeast protein which each ASPES domain is most similar to, such meaningful protein names - rather than abstract GI or RefSeq identifiers - will be extremely helpful when it comes to analysing conservation or phylogeny.
The other feature is of course the full-length sequence of the ASPES domain. Unfortunately BLAST being a local-alignment algorithm does not guarantee that it will not shave off significant bits and pieces from the termini.
Defining the most similar ASPES domain in yeast
This requires to take all sequence identifiers, use their APSES domains and search them against the yeast genome. I actually have given up on finding a Web-tool to do this. Of course this can be done manually, through Blinks - but having to do this for 70 sequences was an uninspiring prospect. And it seems there are no BLAST Webservices that will accept batch-input of lists of sequences.
The full-length protein sequences were copied from the previously prepared input file of [[All_APSES_proteins|86 proteins] and pasted into the input form of the EBI ClustalW service. While this is no longer considered state-of-the-art for multiple sequence alignments, it is computationally efficient and sufficiently accurate for the purpose of approximate domain boundary definition. What we want to construct an input file for aligning just the APSES domains: this should contain the following
- our yeast APSES domain (this defines the boundaries of the domain we are interested in)
- enough sequence extending it N- and C-terminally for the other proteins to ensure we are not throwing out conserved amino acids
- but not too much, since irrelevant sequence can cause problems for the alignment.
Scrolling through the ClustalW result page, the alignment blocks containing the Mbp1 APSES domain sequence were copied and pasted into a MSWord test document, then manually edited to contain only the APSES domains plus some 10 or 20 residues on each end. Through some simple replace commands, this was then brought into a FASTA format. What's a bit annoying is that this changes the headers to contain only the first word (in our case mostly the GI number) .. i.e. from a FASTA input of ...
>6320147 NP_010227.1 Mbp1p [Saccharomyces cerevisiae] MSNQIYSARYSGVDVYEFIHST...
... we get a Clustal record of ...
6320147 --------------------------------------MSNQIYSARYSGVDVYEFIHST 22
...which we can change back into a FASTA record:
>6320147 MSNQIYSARYSGVDVYEFIHST
Tuhs losing part of the header information. There is no easy way to repair the headers in MSWord, but using a trivial perl program this can be automated:
However I consider this cosmetics - the file would have been just as valid with only the GI numbers in the header. Here is the resulting FASTA file containing only APSES domains:
