Computational prediction to identify Medicago truncatula transporters. We used Basic Local Alignment Search Tool (BLAST) and HMMER searches in computational predictions to identify M. truncatula transporters. First, we used the transport protein sequences of Arabidopsis thaliana and the Transporter Classification Database (TCDB) to conduct a BLAST search with M. truncatula protein sequences, provided by the International Medicago Genome Annotated Group (IMGAG). The preprocess data were then analyzed for the presence of a potential transmembrane domain (TMD) using two algorithms: TMHMM and HMMTOP 2.0. Afterward, we used the annotated sequences to conduct a HMMER search with the Pfam annotations from the Pfam database, version 24.0. In addition, all original transporters were compared with proteins of the M. truncatula transporter annotation at the Noble Foundation. We used Perl scripts to analyze the results.
Miao et al. BMC Genomics 2012 13:60 doi:10.1186/1471-2164-13-60