MarkerMiner

Description

markerminer website

MarkerMiner identifies clusters of single-copy gene transcripts present in each user-provided transcriptome assembly by aligning and filtering transcripts against a user-selected reference proteome database. MarkerMiner then generates a detailed tabular report of results. Next, MarkerMiner runs each of the single-copy gene clusters through a multiple sequence alignment (MSA) step using MAFFT (Katoh and Standley 2013) and it outputs MSA files that users can use to assess phylogenetic utility (e.g. sequence variation) or, if appropriate, to conduct preliminary phylogenetic analyses. Lastly, each of the single-copy gene MSAs are re-aligned with MAFFT (using the ‘--add’ functionality; Katoh and Frith 2012) profile alignment step using a user-selected coding reference sequence with intronic regions represented as Ns. Users can use MarkerMiner’s profile alignment output to identify putative splice junctions in the transcripts and to design primers or probes for targeted sequencing.

Environment Modules

Run module spider markerminer to find out what environment modules are available for this application.

Environment Variables

• HPC_MARKERMINER_DIR - installation directory
• HPC_MARKERMINER_BIN - executable directory

Categories

biology, genomics