I am a newbe in Molecular Evolution, but I think many people have faced the problem of harvesting a good collection of orthologous sequences for the same gene (different species - same gene). I always look for this data at NCBI databases. I wonder if there are some tools or pieces of code to automate this work. The final idea is to get a multiple DNA alignment from a single PDB file.
Unlike homology searches, orthology inference is not such a straigth-forward task. One has to be careful to distinguish paralogs from orthologs. Several large orthology projects exist and can be used to assemple a set of paralogs for a given sequence. For example, Ensembl, OMA, Inparanoid, eggNOG, etc. They all have different properties (coverage, accuracy, power) and depending on your final aims you may pick one or several of them to use. You could get an overview of this in a recent review by Altenhoff & Dessimoz (2012) in the book I recently edited (Evolutionary genomics: statistical and computational methods):
http://link.springer.com/protocol/10.1007/978-1-61779-582-4_9
The book itself (2 volumes) has many other chapters that may be useful for other tasks in genomic analyses:
http://www.springer.com/biomed/human+genetics/book/978-1-61779-581-7
http://www.springer.com/biomed/human+genetics/book/978-1-61779-584-8
Unlike homology searches, orthology inference is not such a straigth-forward task. One has to be careful to distinguish paralogs from orthologs. Several large orthology projects exist and can be used to assemple a set of paralogs for a given sequence. For example, Ensembl, OMA, Inparanoid, eggNOG, etc. They all have different properties (coverage, accuracy, power) and depending on your final aims you may pick one or several of them to use. You could get an overview of this in a recent review by Altenhoff & Dessimoz (2012) in the book I recently edited (Evolutionary genomics: statistical and computational methods):
http://link.springer.com/protocol/10.1007/978-1-61779-582-4_9
The book itself (2 volumes) has many other chapters that may be useful for other tasks in genomic analyses:
http://www.springer.com/biomed/human+genetics/book/978-1-61779-581-7
http://www.springer.com/biomed/human+genetics/book/978-1-61779-584-8
Steps
1. Take your query sequence and blast with desired database
2. filter the blast result with suitable e-value (usually 10^-4 to 10^-6) and query coverage (if multiple sequence matched with same e-value for same strain)
3. Reblast with the resulted sequence to see if the original sequence (your query) return (Reciprocal blast)
If all goes successfully you will find your orthologous gene sets
To be sure
1. Test for paralogous detection (RDP is best for this one)
2. Text for xenologous detection (can use T-Rex)
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