I apologize for asking a very basic question.
Using local BLAST searches against a genome, I am trying to retrieve full length homologous sequences of a gene of interest. Ultimately, I am interested in knowing the copy number of these genes and would also like to retrieve pseudogenes, if any. However, BLAST search (tblastn; BLAST 2.2) against the downloaded genomes (e.g., M. martensii: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AYEL01#contigs) is retrieving several partial hits. I wonder if it is because I am BLAST searching against a collection of contigs and not against an assembled scaffold. Do I need to assemble these contigs into scaffolds before BLAST searching or are these files available elsewhere? Alternately, is there any tool that would be beneficial in this process?
Thank you very much in advance,