Explanation of how to efficiently use the TAIR database for finding homologs of cDNA? BLAST, FASTA, Wu-BLAST

Question

[zak4.0]

I have an assignment to do that involves using the cDNA obtained from Olest23, which is a gene that is induced upon infection. My professor and their team found this while working on olive trees. We dont have a complete genome of olive trees so now I need to find homologs using arabidopsis by utilizing the TAIR database. Unfortunately genetics is one of my worst subjects, as is plant biology so Im not even certain what Im actually looking for when using BLAST, FASTA, and WU-BLAST to find a homolog of the cDNA sequence that ive been given (along with the deduced amino acid sequence). I dont really know anyone at my uni so I dont have the opportunity to talk it out with. If anyone could give me a little direction on how to effectively use these tests I would definitely appreciate it.

Answer 1

[Denise CS]

FASTA is a text file format for sequences (whether nucleotide or amino acid) and starts with the '>' followed by a header. BLAST allows you to search for similarities between your cDNA sequence (in FASTA format, for example), which is the query sequence, versus the genome (the target). WU-BLAST (WU is for Washington University) is a type of BLAST and so is NCBI-BLAST. The former seems to have retired according to this note. If you want to run the NCBI-BLAST search using your olive cDNA sequence against the Arabidopsis thaliana genome you can use the BLAST in Ensembl Plants web interface. You can also search for similarities against many other plant genomes there, not just A. thaliana. For more details on running the BLAST web interface in Ensembl, check this video and help pages.

Answer 2

[mastal511]

This BLAST documentation from the NCBI BLAST website might be a good place to start.

http://www.ncbi.nlm.nih.gov/books/NBK153387/

There is also lots of other information/documentation on the NCBI BLAST pages.