Tag: Identify

FINDSIRE – Identify Mothers or Sires

FINDSIRE

:: DESCRIPTION

FINDSIRE has emerged from the large scale paternity testing project performed on the rhesus macaques of Cayo Santiago (Nuernberg et al. 1998, Am J Primatol 44, 1-18). The software allows to identify mothers or sires by means of the comparison of a large number of potential parents, typed at single locus DNA markers, with given infants or parent-infant duos. Potential parents with more than a certain number of mismatches in their DNA profiles are excluded from parenthood whilst those not excluded are reported for further analysis.

::DEVELOPER

 Michael Krawczak

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

   FINDSIRE

:: MORE INFORMATION

Pathicular 1.55 – Cytoscape plug-in of Identifies Path Motifs

Pathicular 1.55

:: DESCRIPTION

Pathicularis the Cytoscape plug-in which identifies path motifs in integrated networks and arranges them in a modular structure. After the integrated network and the source network (deletion or overexpression in this case) are loaded into Cytoscape, Pathicular can be used to find all the paths of a given type in the source network using the integrated network. A p-value is provided to check the overrepresentation of the path of interest.

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Pathicular

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(3):R32. Epub 2010 Mar 11.
Characterizing regulatory path motifs in integrated networks using perturbational data.
Joshi A, Van Parys T, Peer YV, Michoel T.

noisy 1.5.12 – Identify Homo-plastic Characters in Multiple Sequence Alignments

noisy 1.5.12

:: DESCRIPTION

Noisy is a software to identify homo-plastic characters in multiple sequence alignments.In a first phase the rows of the input multiple sequence alignment (MSA) in multi fasta format are reordered to conform to a circular ordering. For this purpose noisy includes the corresponding subset of routines from David Bryant and Vincent Moulton’s NeighborNet and Stefan Grünewald’s QNet packages. Subsequently, a reliability score for each column of the reordered MSA is calculated. Essentially, the number of character state alterations in an alignment column is counted and compared to the observed count in random shufflings of the column. The uniform pseudo-random number generator Mersenne Twister is used to generate the random shufflings of alignment columns.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 noisy

:: MORE INFORMATION

Citation

Andreas W. M.Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
Noisy: identification of problematic columns in multiple sequence alignments.
Algorithms Mol Biol, 3:7 (2008).

Spotter 0.5 – Identify Region of Interest near Associated Variant

Spotter 0.5

:: DESCRIPTION

Spotter is a program for identifying a region of interest (using LD and recombination) near an associated variant.

::DEVELOPER

Ryan Welch (welchr@umich.edu) at the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Spotter

 

:: MORE INFORMATION

Please take the time to register so we might notify you of future changes.

SIBMED 1.0 – Identify Likely Genotyping Errors and Mutations

SIBMED 1.0

:: DESCRIPTION

SIBMED ((SIBpair Mutation and Error Detection)) is a FORTRAN 77 program that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping.Specifically, using a hidden Markov model, the program calculates the posterior probability of genotyping error or mutation for each sib-pair-marker combination, given all the available marker data, an assumed genotype-error rate, and a known genetic map.  The subset of combinations for which this posterior error probability is high may be considered for exclusion, review, or retyping.

::DEVELOPER

the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • FORTRAN

:: DOWNLOAD

  SIBMED

:: MORE INFORMATION

Citation

Douglas JA, Boehnke M, Lange K (2000)
A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data.
Am J Hum Genet 66: 1287-1297

OFF-TARGET PIPELINE 1.5.4.2 -Identify Off-targets of Pharmaceuticals

OFF-TARGET PIPELINE 1.5.4.2

:: DESCRIPTION

OFF-TARGET PIPELINE is a platform intended to carry out a recently introduced chemical systems biology approach for secondary target identification, but may also be useful to other applications in bioinformatics and drug discovery. Researchers can predict and compare protein functional sites, conduct structure-based docking, compute binding energy and compare electrostatic potential distribution within cavities. It also supports normalization of docking scores, information retrieval from PDB, and parsing of output files. All the afore-mentioned procedures are parallelized with significant speed gains and labor savings.

::DEVELOPER

Thomas Evangelidis (tevang3@gmail.com)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 OFF-TARGET PIPELINE

:: MORE INFORMATION

References:

L. Xie, J. Wang and P.E. Bourne 2007
“In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators“.
PLoS Comp. Biol., 3(11):e217