The metagenomic paradigm allows for an understanding of the
metabolic and functional potential of microbes in a community via a study
of their proteins. The substrate for protein identification is either the
set of individual nucleotide reads generated from metagenomic samples or
the set of contig sequences produced by assembling these reads. However, a
read-based strategy using reads generated by Next Generation Sequencing
(NGS) technologies, results in an
overwhelming majority of partial-length protein predictions. A nucleotide
assembly-based strategy does not fare much better since metagenomic
assemblies are typically very fragmented and also leave a large fraction
of reads unassembled. Here we present an assembly strategy that allows for
the reconstruction of complete protein sequences directly from the NGS
reads. We also introduce a novel strategy for the accurate identification
of homologs of a query protein sequence in a metagenomic database of short
protein fragments.