http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/
Genetic Analysis Software--Genetic Analysis Software Your Logo END of COMMENT--Pubmed Entrez BLAST OMIM Taxonomy Structure Downloads FASTLINK MSA CASPAR Pedhunter (genealogy in Sybase) Pedhunter (genealogy in text_files) CGH software Mapping software References Overview Richa Agarwala and Alejandro Schäffer are working together and separately on various software_packages for analysis of genetic data. This page briefly summarizes several ongoing projects and provides hyperlinks to a more detailed page about each project, download software, and references for papers. Summary of ongoing projects FASTLINK Alejandro Schäffer has_led the development of the FASTLINK software_package for genetic linkage analysis. Genetic linkage analysis is a statistical technique used to map genes and find the approximate locations of disease genes. FASTLINK aims to replace the main programs of the widely used package LINKAGE by doing the same computations faster. FASTLINK can also run in_parallel either on a shared-memory computer or on a network of workstations. FASTLINK adds much new documentation. FASTLINK has_been_used in over 600 published genetic studies. FASTLINK is freely available by ftp; follow the hyperlink to the FASTLINK page for more details. MSA In_collaboration with Sandeep Gupta, Alejandro Schäffer developed a significantly faster and more space-efficient version of the program MSA to do multiple sequence alignment. Follow the hyperlink to the MSA page to retrieve the paper and software. CASPAR Richa Agarwala, Jeremy Buhler (Washington U), . and Alejandro Schäffer have_developed software to do conditional linkage analysis of polygenic diseases such_as diabetes, asthma, and glaucoma. The software is_called CASPAR (Computerized Affected Sibling Pair Analyzer and Reporter). Other participants in the design of CASPAR are: Kenneth Gabbay (Baylor College of Medicine), Prof. Marek Kimmel (Rice_university) and David Owerbach (Baylor College of Medicine. Follow the hyperlink to the CASPAR page to retrieve the software. Pedhunter Richa Agarwala has_developed software called Pedhunter to query a genealogical database. Among the problems Pedhunter solves is how best to connect a set of relatives with the same disease into a pedigree suitable for input to genetic linkage analysis. Pedhunter is currently being_used at NCBI to query the Amish Genealogy database (AGDB), a database of over 295,000 members of the Amish and Mennonite religious groups, and their relatives. Other participants in the design of Pedhunter and AGDB include Leslie Biesecker (NHGRI/NIH Clair Francomano (now at NIA/NIH), and Alejandro Schäffer. Pedhunter is being_used by other research groups to query other genealogical databases. Pedhunter query software comes in two flavors that depend_on how the genealogy is_stored: in a SYBASE database or in ASCII_TEXT_FILES. Follow one of the two Pedhunter hyperlinks to retrieve a paper and software. Software to analyze comparative genomic hybridization data Richard Desper (now at NCBI) and Alejandro Schäffer have_developed software to analyze data on tumors to study models of oncogenesis. The software is_designed to analyze data generated by a technique called comparative genomic hybridization, but it has also been_used to analyze cytogenetic breakpoint data. The focus of the software is to infer tree models that relate genetic aberrations to tumor progression. Participants in the design of the software include Olli Kallioniemi (NHGRI/NIH) and Christos Papadimitriou (UCBERKELEY). Software for radiation hybrid mapping and map integration Richa Agarwala developed software to construct radiation hybrid maps and to integrate maps that contain overlapping marker sets. The radiation hybrid mapping methods are based_on: a new strategy to select framework markers, a known reduction from the radiation hybrid mapping problem to the traveling_salesman problem, and using the existing software CONCORDE to solve large instances of the traveling_salesman problem. The map construction software was_used at NCBI to construct dense human radiation hybrid maps. Follow the link on the right to learn more about these maps. Participants at NCBI include Donna Maglott, Greg Schuler, and Alejandro Schäffer. David Applegate, co-developer of CONCORDE, collaborated on_its usage for radiation hybrid map construction. Details FASTLINK MSA CASPAR Pedhunter CGH Software RH map construction Downloads FASTLINK Pedhunter CASPAR END COMMENT--Help Search NLM NIH Disclaimer