NeuroPIpred – Tool to Predict, Design and Scan Insect Neuropeptides

NeuroPIpred

:: DESCRIPTION

NeuroPIpred is an in silico method, which is developed to predict and design insect neuropeptides with better efficacy for controlling pest from infesting various crops.

::DEVELOPER

NeuroPIpred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

NeuroPIpred: a tool to predict, design and scan insect neuropeptides.
Agrawal P, Kumar S, Singh A, Raghava GPS, Singh IK.
Sci Rep. 2019 Mar 26;9(1):5129. doi: 10.1038/s41598-019-41538-x.

selscan 1.1.0b – EHH-based Scans for Positive Selection

selscan 1.1.0b

:: DESCRIPTION

selscan is a program to calculate EHH-based scans for positive selection in genomes

::DEVELOPER

The Hernandez Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 selscan

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 Oct;31(10):2824-7. doi: 10.1093/molbev/msu211. Epub 2014 Jul 10.
selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.
Szpiech ZA, Hernandez RD

SCAN-UPC 2.10.0 – Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

SCAN-UPC 2.10.0

:: DESCRIPTION

Single Channel Array Normalization (SCAN) is a microarray normalization method to facilitate personalized-medicine workflows.

The Universal Probability of expression Codes (UPC) method is an extension of SCAN that produces “probabilistic barcode” values that estimate the probability a given gene is active in a specific sample.

SCAN and UPC are currently implemented in the SCAN-UPC.

::DEVELOPER

W. Evan Johnson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R Package
  • BioConductor

:: DOWNLOAD

 SCAN-UPC

:: MORE INFORMATION

Citation

Genomics. 2012 Dec;100(6):337-44. doi: 10.1016/j.ygeno.2012.08.003.
A single-sample microarray normalization method to facilitate personalized-medicine workflows.
Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, Johnson WE.

RASTA-Bacteria – Rapid Automated Scan for Toxins and Antitoxins in Bacteria

RASTA-Bacteria

:: DESCRIPTION

RASTA-Bacteria is an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not.

::DEVELOPER

GenOuest

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Genome Biol. 2007;8(8):R155.
RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes.
Sevin EW, Barloy-Hubler F.

SCANSTAT – Scan Statistics for Disease Gene Association of a set of Contiguous SNPs

SCANSTAT

:: DESCRIPTION

SCANSTAT considers a number of marker loci in the genome. At each marker, genotypes are available for two types of observations

::DEVELOPER

Jurg Ott, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SCANSTAT

:: MORE INFORMATION

Citation

Scan statistics to scan markers for susceptibility genes.
Hoh J, Ott J.
Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9615-7.

SeqCNVCBS 1.0 – Scan Statistics for CNV Detection with CBS

SeqCNVCBS 1.0

:: DESCRIPTION

SeqCNVCBS is for the use of detecting Copy Number Variation (CNV) using sequencing data. Matched-samples of control and case (normal and tumor) are required. The algorithm uses a scan statistics to detect windows of rate differences in two non-homogeneous Poisson Processes.

::DEVELOPER

Jeremy J. ShenNancy R. Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • R Package

:: DOWNLOAD

  SeqCNVCBS

:: MORE INFORMATION

AUTOSCAN 1.0.3 – Easy Genome-wide Scans with Analyze

AUTOSCAN 1.0.3

:: DESCRIPTION

AUTOSCAN automatically creates data files, uses MAKEPED (converts pre-linkage format files to linkage format), DOWNFREQ (estimates allele frequencies from pedigree data), and PEDCHECK (Mendelian checking) programs and finally starts statistical analyses via the ANALYZE package. ANALYZE performs parametric linkage analysis (MLINK), nonparametric affected sib-pair analysis (ASP), family-based association analysis (TDT, HRRR), and homogeneity testing (HOMOG). Input files for AUTOSCAN are the pedigree files for all chromosomes,the disease model file, the number of loci file, and the ANALYZE input file.The AUTOSCAN also allows easy handling of several phenotype traits and trait features by only changing the disease model file after each run.

::DEVELOPER

Tero Hiekkalinna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD AUTOSCAN

AUTOSCAN

:: MORE INFORMATION

N/A

CisModScan 20050417 – Scan for Cis-regulatory Modules given PWMs

CisModScan 20050417

:: DESCRIPTION

CisModScan: Scanning for cis-regulatory modules with given motif weight matrices.

::DEVELOPER

Qing Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 CisModScan

:: MORE INFORMATION

Related papers:
1) Johnson, D.S., Zhou, Q., Yagi, K., Satoh, N., Wong, W.H., and Sidow, A. (2005). De dovo discovery of a tissue-specific gene regulatory module in a chordate. Genome Research, 15: 1315-1324.
2) Zhou, Q. and Wong, W.H. (2004). CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proceedings of the National Academy of Sciences USA, 101: 12114-12119.