Graduate student, University of Maryland, College Park
A method to detect conclusively whether and when a sequence is similar to a database of sequences
An important task in microbiome study is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare the sequence in the sample to a database of known sequences. The sequence search software like BLAST gives the list of sequences from the database in the order of the match quality. When the sequences are closely related to sequences in the database, it is easier to assign a taxonomic label based on those sequences, but when sequences more diverse it is tricky to decide which of the top scoring matches are relavant. In this work, we develop a method that can conclusively decide whether and when a sequence is similar to the sequences in the database.
Abstract: The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
Pub.: 23 Apr '05, Pinned: 28 Jun '17