2.
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Bioinformatics.
2016 Aug 15; 32(16): 2520-3. Epub 2016 Apr 8; PubMed:
27153620.Abstract + PDF
MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes.
1.
Benchmarking the next generation of homology inference tools.
Saripella GV, Sonnhammer EL, Forslund K
Bioinformatics.
2016 Jun 1; [Epub ahead of print] PubMed:
27256311.Abstract + PDF
Over the last decades, vast numbers of sequences were deposited in public databases. Bioinformatics tools allow homology and consequently functional inference for these sequences. New profile-based homology search tools have been introduced, allowing reliable detection of remote homologs, but have not been systematically benchmarked. To provide such a comparison, which can guide bioinformatics workflows, we extend and apply our previously developed benchmark approach to evaluate the "next generation" of profile-based approaches, including CS-BLAST, HHSEARCH and PHMMER, in comparison with the non-profile based search tools NCBI-BLAST, USEARCH, UBLAST and FASTA.