:: DESCRIPTION
Patser scores the L-mers (subsequences of length L) of the indicated sequences against the indicated alignment or weight matrix.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SRF (Spectral Repeat Finder) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2004 Jun 12;20(9):1405-12. Epub 2004 Feb 19.
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.
Sharma D, Issac B, Raghava GP, Ramaswamy R.
:: DESCRIPTION
Electronic Periodic Table – simple, friendly and really handy freeware tool that lets you find and view details and properties for every chemical element.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ChIPSeqPeakFinder (ChIPSeq Peak Finder) is a tool to find peaks from ChIPSeq data generated from the Solexa / Illumina platform. Optionally, data from the peaks found can also be exported to simple textfile format for further usage.
:: DEVELOPER
Computational & Mathematical Biology Lab @ GIS
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen X. et al. (2008)
“Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells“.
Cell, Volume 133, Issue 6, 1106-1117,
:: DESCRIPTION
FASTA Composition finds the overall composition of sequences in a FASTA file.
::DEVELOPER
Statistical Computational Biology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.
::DEVELOPER
Theoretical Life Sciences Research Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhao Xu, Hao Wang,
“LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons“,
Nucleic Acids Res. 2007 July; 35(Web Server issue): W265-W268.
:: DESCRIPTION
PatMatch (Pattern Matching) allows you to search for short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns. It uses the same Arabidopsis dataset as TAIR’s BLAST and FASTA programs. If you are searching for a sequence >20 bp or aa with no degenerate positions, please use BLAST or FASTA, which are much faster. Pattern Matching allows for ambiguous characters, mismatches, insertions and deletions, but does not do alignments and so is not a replacement for BLAST and FASTA Currently the maximum number of hits retrieved is 250,000 and the minimum number of input string is 3 residues.
::DEVELOPER
The Arabidopsis Information Resource
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY.
PatMatch: a program for finding patterns in peptide and nucleotide sequences.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W262-6.
:: DESCRIPTION
Glob-mapper is required to plot Event-mapper and Peak-mapper data and to extract hot spots (gene clusters) from the Event maps. Glob-mapper will search for the input data in a directory with pre-computed *.dat and *.sgn files generated by Event- or Peak-mapper, Glob-mapper also requires an identification file, containing genes ID and other information (a sample file is provided). This information will be displayed for the extracted genes. The ID file must contain at least three columns of data: 1 – unique profile identifier, 2 – gene identifier or CG number, this information will be extracted, 3 (must be the last column) – user-defined score value, this value is used to display a subset of the entire data on Event maps. Using this value user can, for instance, display all genes of a given pathway, which may serve as a marker in the analysis of the global gene expression.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.
:: DESCRIPTION
Peak-mapper is the program to identify local differences (disconcordances) in gene expression after aligning orthologous data sets. The program takes two aligned microarray datasets (*.aln) as an input and returns a map similar to that of Event-mapper, where peaks (hot spots) correspond to gene batteries having similar disconcordances between two organisms.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.
:: DESCRIPTION
AVF-filter is designed for the removal of noisy/low-variance expression profiles and non-periodic profiles (optional, for cell culture data).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.
