REPFIND 20040309 – Find Clustered, Exact Repeats in Nucleotide Sequences

REPFIND 20040309

:: DESCRIPTION

REPFIND is a program to find clustered, exact repeats in nucleotide sequences. For each repeat cluster that it finds, it calculates a P-value, which indicates the probability of finding such a concentration of that particular repeat just by chance. Of the many possible clusters for each repeated word, REPFIND selects the one with the most significant P-value.

We are using REPFIND to study localization of messenger RNAs. These molecules sometimes contain signals in their 3′ untranslated regions that specify how they are transported in the cell, prior to being translated. This process is essential for establishing body axes in embryogenesis, among other things. The localization signals often appear to consist of repeat clusters that can be detected by REPFIND.

::DEVELOPER

the Center for Advanced Genomic Technology

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

REPFIND

:: MORE INFORMATION

REPFIND Online Version

Citation:

JN Betley, MC Frith, JH Graber, S Choo, JO Deshler (2002). A ubiquitous and conserved signal for RNA localization in chordates. Current Biology, 12, 1756-61.

Motif Search 0.2

Motif Search 0.2

:: DESCRIPTION

A simple motif searcher. No matrices, nothing fancy, just simple searching for base strings. Allows degenerate bases to be used.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Motif Search ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

LOCK 1.2 – Locater of Oligos

LOCK 1.2

:: DESCRIPTION

LOCK Locates user-specified oligonucleotide patterns within a larger sequence. For example, restriction digest sites and fragment sizes can be determined for a plasmid or genome.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac Os / Linux
  • Perl
  • TK

:: DOWNLOAD

LOCK ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

FOCK 1.0 – Frequency of Oligos

FOCK 1.0

:: DESCRIPTION

FOCK Analyzes a FASTA sequence for n-mer frequency (specified by user). Useful for identifying common or rare restriction sites, etc.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

Command-line interface.

:: REQUIREMENTS

:: DOWNLOAD

FOCK for Win ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

DRACK 3.1 – Differential Restriction Analysis

DRACK 3.1

:: DESCRIPTION

DRACK takes up to 6 FASTA DNA sequence files as input and outputs a tab-delimited text file containing sizes of restriction fragments (which can be opened in a spreadsheet program). Several options are available, including 4-6 base cutters and running in differential or list-all cutters mode. Differential analysis will analyze the sequences and only output restriction enzymes which distinguish between the sequences, while listing all cutters will list even those cutters which do not distinguish between the sequences. This program’s primary purpose was to automatically choose sites to distinguish plasmid clones with an insert in two possible orientations.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

DRACK ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

SilVA 1.1.1 – Silent Variant Analysis using random Forests

SilVA 1.1.1

:: DESCRIPTION

SilVA (Latin for “forest”) is a tool for the automated harmfulness prediction of synonymous (silent) mutations within the human genome. SilVA bases its predictions on a number of features, including conservation, codon usage, splice sites, splicing enhancers and suppressors, and mRNA folding free energy. Given variants in a VCF file, SilVA will rank the rare synonymous variants according to their predicted harmfulness.

::DEVELOPER

Orion Buske and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl
  • Python
  • R package

:: DOWNLOAD

 SilVA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1843-50. doi: 10.1093/bioinformatics/btt308.
Identification of deleterious synonymous variants in human genomes.
Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M.

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