Identifying genes from contigs

[contact_monu]

Hello All,

I have got a fasta file containing a list of contigs which were obtained through transcriptome analysis. Now, I want to find the gene of my interest from these contigs. What I am doing at present is that I have performed a blastx of these contigs against nr database and have obatined hits matching to my gene of interest. Now the question is that sometimes I get the query frame from blastx result to be negative, so shall I reverse complement the sequence and take it as a gene sequence ? Also, I found that match of the query is only to half of the subject sequence, which means that gene sequence may be incomplete ?

Any help would highly appreciated.

Thanks