Journal of Data Mining in Genomics & Proteomics

James A Foster

Publications

• Research Article
  SlopMap: A Software Application Tool for Quick and Flexible Identification of Similar Sequences Using Exact K-Mer Matching
  Author(s): Ilya Y Zhbannikov, Samuel S Hunter, Matthew L Settles and James A FosterIlya Y Zhbannikov, Samuel S Hunter, Matthew L Settles and James A Foster
  
  With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes. With the raw DNA-library of a complete genome it would appear to be a trivial problem to identify reads of interest. But it is not always easy to incorpo-rate well-known tools such as BLAST, BLAT, Bowtie, and SOAP directly into a bioinformatics pipelines before the assembly stage, either due to in-compatibility with the assembler’s file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order to incorporate flowgrams from a Roche 454 sequencer into the Newbler assembler it is neces.. View More»
  DOI: 10.4172/2153-0602.1000133

  Abstract PDF