SeSAW 2.0 – Functional Mapping by Sequence-Derived Structural Alignment Weights

SeSAW 2.0

:: DESCRIPTION

SeSAW (sequence-derived structural alignment weights) is a web-based program for identifying functionally or evolutionarily conserved motifs in protein structures by locating sequence and structural similarities, and quantifying these at the level of individual residues. Results can be visualized in 2D, as annotated alignments, or in 3D, as structural superpositions. An example is given for both an experimentally determined query structure and a homology model.

::DEVELOPER

Department of Genome Informatics; Research Institute for Microbial Diseases; Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

SeSAW: balancing sequence and structural information in protein functional mapping.
Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H.
Bioinformatics. 2010 May 1;26(9):1258-9. Epub 2010 Mar 17.

3FunMap 1.0 – Full-sib Family Functional Mapping tools

3FunMap 1.0

:: DESCRIPTION

3FunMap is a Windows software that can be used to construct genetic linkage maps and perform functional QTL mapping with molecular markers generated in a full-sib family. For linkage analysis, the software utilizes seven segregation types of markers to estimate the recombination and simultaneously predict the linkage phase between any two markers. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating local ordering methods. Multi-locus linkage phases for the optimal order of each linkage group are predicted based on three-point linkage analysis.

::DEVELOPER

Center for Statistical Genetics, Penn State University

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

3FunMap

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2006-8. doi: 10.1093/bioinformatics/btr306. Epub 2011 May 17.
3FunMap: full-sib family functional mapping of dynamic traits.
Tong C, Wang Z, Zhang B, Shi J, Wu R.

FMAP – Functional Mapping and Analysis Pipeline for Metagenomics and Metatranscriptomics studies

FMAP

:: DESCRIPTION

FMAP (Functional Mapping and Analysis Pipeline) is an open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data.

::DEVELOPER

The Quantitative Biomedical Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Perl

:: DOWNLOAD

FMAP

:: MORE INFORMATION

Citation

Kim J, Kim MS, Koh AY, Xie Y, Zhan X.
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
BMC Bioinformatics. 2016 Oct 10;17(1):420.PMID: 27724866

Funmap 2.2.1 – Functional Mapping Package for R

Funmap 2.2.1

:: DESCRIPTION

The Funmap package is developed to identify quantitative trait loci (QTL) for a longitudinal, or vectorized, phenotypic trait as based on the Funmap model

::DEVELOPER

Center for Statistical Genetics, Penn State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows /Linux/ MacOsX
R package

:: DOWNLOAD

Funmap

:: MORE INFORMATION

Citation

Ma, C. X., G. Casella, and R. L. Wu, 2003.
Functional mapping of quantitative trait loci underlying the character process: A theoretical framework.
Genetics 161(4): 1751-1762.