MetaMap is a highly configurable program to map biomedical text to the UMLS Metathesaurus or, equivalently, to discover Metathesaurus concepts referred to in text. MetaMap uses a knowledge-intensive approach based on symbolic, natural-language processing (NLP) and computational-linguistic techniques. Besides being applied for both IR and data-mining applications, MetaMap is one of the foundations of NLM’s Medical Text Indexer (MTI) which is being used for both semiautomatic and fully automatic indexing of biomedical literature at NLM.
Dr. Alan (Lan) Aronson at the National Library of Medicine (NLM)
DamMet is probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen. The model is implemented as a two step procedure. The first step recovers a maximum likelihood estimate (MLE) of the position specific deamination rates for methylated and unmethylated cytosine residues. The second step, making use of these deamination rates, returns a MLE of the methylation level in a user-defined genomic window. The software is multithreaded
BSMAP（Bisulfite Sequence Mapping Program）is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.
Identitag is a tool called for tag-to-gene mapping. This tool is based on a relational database which structure can be depicted as three interconnected modules represented in Identitag relational schema. The first one stores virtual tags extracted from transcript sequences belonging to the species considered the second stores experimental tags observed in SAGE experiments, and the third allows the annotation of the transcript sequences used for virtual tag extraction. Identitag therefore connects an observed tag to a virtual tag and to the transcript sequence from which it is derived, and then to its functional annotation when available. For a complete description of Identitag tables see Identitag data dictionary.
CORA is a compressive-acceleration tool for NGS read mapping methods. When plugged into existing mapping tools, CORA achieves substantial runtime improvement through the use of compressive representation of the reads and a comprehensive homology map of the reference genome.