metameta is a toolset for analyzing metatranscriptome data that has been mapped to metagenomic data.

As high-throughput sequencing data becomes more prominent, the issue of mining the wealth of data
continually arises. Many  programs such as PROKKA have addressed this issue in many regards but most
of these tools focus on annotation or statistical analysis of metagenomic data. Alignment and annotation
data reveals previously discovered genes present in a sample and can identify nucleotide segments with
features characteristic of genes with no known equivalent. Annotations of metatranscriptomic data 
identifies proteins or ncRNA being transcribed and may reveal novel sequences. Statistical analysis 
of metagenomic/transcriptomic data can elucidate the relative abundance of short reads and thus their 
products. Such statistical tools can compare samples and, when utilized on metatranscriptomic data,
can reveal what proteins and ncRNAs are being expressed in specific environments.

Neither of these methods, however, correlate expression patterns with genomic sequences. By analyzing
metatranscriptome short reads mapped onto assembled metagenomes, one can identify expression
patterns of neighboring genes and/or operons. This information reveals not just genes present and/or
expressed in a given sample, but the presence and expression of pathways. This method also permits easy
identification of actively transcribed novel genes via the mapping of metatranscriptome short reads
onto segments of metagenome assemblies without any known homolog. Metagenomic sequences coding
for genes, as identified by metatranscriptome data, can be extrapolated to nearby start and stop codons
to ensure that entire gene products are identified.

In short, mapping metatransctipome data onto metagenome data has many clear advantages over previous
analysis techniques. This mapping is easily performed with existing programs such as BWA and BLAST.
metameta offers a toolset to analyze the mapping data using both existing software and original code.