Tag: Fingerprint

FAMD 1.31 – Dominant Fingerprint Data Handling and Analysis

FAMD 1.31

:: DESCRIPTION

FAMD (Fingerprint Analysis with Missing Data)  is an easy-to-use general-purpose program for dominant fingerprint data handling and analysis (explicitly allowing ambiguities/missing data points) with a graphical user interface, supporting flexible data input and export to a variety of formats. Analysis capabilities include distance-based analysis (trees and PCoA, with graphical 3D viewer), bootstrapping and consensus tree generation, allele frequency estimation, AMOVA, inter-population distances, Shannon’s index.

::DEVELOPER

Dr.  Philipp  Schlüter

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 FAMD

:: MORE INFORMATION

Citation:

Schlüter, P. M. & Harris, S. A., 2006,
Analysis of multilocus fingerprinting data sets containing missing data.
Mol. Ecol. Notes. 6: 569-572.

AllergenFP 1.0 – Allergenicity Prediction based on a novel descriptor Fingerprint Approach

AllergenFP 1.0

:: DESCRIPTION

AllergenFP is a bioinformatics tool for allergenicity prediction based on a novel descriptor fingerprint approach

::DEVELOPER

Drug Design Group, Medical University of Sofia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 15;30(6):846-51. doi: 10.1093/bioinformatics/btt619. Epub 2013 Oct 27.
AllergenFP: allergenicity prediction by descriptor fingerprints.
Dimitrov I1, Naneva L, Doytchinova I, Bangov I.

ProteinDecision 1.0 – Protein Identification using Peptide-Mass Fingerprinting Data

ProteinDecision 1.0

:: DESCRIPTION

ProteinDecision is a computer software for identifying protein by serching against protein database with the input Peptide-Mass Fingerprinting Data. It can handle the issues of selecting peaks from mass spectrum, transforming database format, displaying the top ranks of identification result, and detailed information for each ranking.

::DEVELOPER

Digital Biology Laboratory, University Of Missouri-Columbia

:: SCREENSHOTS

ProteinDecision

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 ProteinDecision

:: MORE INFORMATION

Citation

Methods Mol Biol. 2010;604:7-22. doi: 10.1007/978-1-60761-444-9_2.
Bioinformatics methods for protein identification using Peptide mass fingerprinting.
Song Z1, Chen L, Xu D.

FPB 1.1 – FingerPrint Background removal

FPB 1.1

:: DESCRIPTION

FPB is a new data-independent tool suitable for large scale projects as well as mapping of few clones.

::DEVELOPER

Istituto di Genomica Applicata

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl
  • TCL/TK

:: DOWNLOAD

 FPB

:: MORE INFORMATION

Citation

Automated FingerPrint Background removal: FPB.
Scalabrin S, Morgante M, Policriti A.
BMC Bioinformatics. 2009 Apr 30;10:127.

LactFP – β-Lactamase Fingerprint Prediction Server

LactFP

:: DESCRIPTION

LactFP find signature in query protein sequence belong to specific b-lactamase family.In response to query protein submission, it finds the family specific pattern.

::DEVELOPER

LactFP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ScientificWorldJournal. 2014 Feb 11;2014:980572. doi: 10.1155/2014/980572. eCollection 2014.
Identification of family specific fingerprints in β-lactamase families.
Srivastava A1, Singhal N2, Goel M1, Virdi JS2, Kumar M

FMTP – Fingerprint-based Minimal Tiling Path

FMTP v1

:: DESCRIPTION

FMTP is a software tool to compute the MTP of a physical map based purely on restriction fingerprint data (and the contigs). FMTP completely ignores the ordering of clones obtained by the physical map algorithm.

::DEVELOPER

Bozdag Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FMTP

:: MORE INFORMATION

Citation

A graph-theoretical approach to the selection of the minimum tiling path from a physical map.
Bozdag S, Close TJ, Lonardi S.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):352-60. doi: 10.1109/TCBB

FASSI 1.0 – Fingerprint and ASSembly Incorporation

FASSI 1.0

:: DESCRIPTION

FASSI (Fingerprint and Assembly Incorporation) is a stand-alone Perl application, that calculates BAC end and BAC overlap length constraints from clone fingerprint map contigs created by the FPC package to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: REQUIREMENTS

:: DOWNLOAD

 FASSI

:: MORE INFORMATION

Citation

Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang S-P, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJM. 2006.
Physical map-assisted whole-genome shotgun sequence assemblies.
Genome Res. 16:768-775

GelQuest 3.1.7 – Analysis of DNA Fingerprints

GelQuest 3.1.7

:: DESCRIPTION

GelQuest is a software for the analysis of DNA fingerprints (AFLP, t-RFLP, RAPD, ERIC-PCR, RFLP-PCR). It works in a fast and efficient way with trace files (FSA files) as well as with gel image files (TIFF, JPG, BMP, etc.) and handles AFLP, t-RFLP, ERIC-PCR, RFLP-PCR or RAPD data.

::DEVELOPER

SequentiX – Digital DNA Processing

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GelQuest

:: MORE INFORMATION

Use  contact form to request a trial license.

FingerPRINTScan – PRINTS Fingerprint Search Tool

FingerPRINTScan

:: DESCRIPTION

The FingerPRINTScan package uses an approach, based on Karlin and Altschul statistics, to generate a probability-value for each scoring match to a motif.

::DEVELOPER

Attwood Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 FingerPRINTScan 

:: MORE INFORMATION

Citation

Bioinformatics. 1999 Oct;15(10):799-806.
FingerPRINTScan: intelligent searching of the PRINTS motif database.
Scordis P, Flower DR, Attwood TK.

FPC 9.4 – Build Contigs from Fingerprinted Clones

FPC 9.4

:: DESCRIPTION

FPC (fingerprinted contigs)is an interactive program for building contigs from fingerprinted clones, where the fingerprint for a clone is a set of restriction fragments.FPC has an algorithm to automatically cluster clones into contigs based on their probability of coincidence score. For each contig, it builds a consensus band (CB) map which is similar to a restriction map but it does not try to resolve all the errors. The CB map is used to assign coordinates to the clones based on their alignment to the map and to provide a detailed visualization of the clone overlap. FPC has editing facilities for the user to refine the coordinates and to remove poorly fingerprinted clones. Functions are available for updating an FPC database with new clones. Contigs can easily be merged, split or deleted. Markers can be added to clones and are displayed with the appropriate contig. Sequence ready clones can be selected and their sequencing status displayed. As such, FPC is an integrated program for the assembly of sequence ready clones for large scale sequencing projects

:: DEVELOPER

Arizona Genomics Computational Lab (AGCoL)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 FPC

:: MORE INFORMATION

Citation:

Nelson, W. and C. Soderlund (2009).
Integrating Sequence with FPC Fingerprinted Maps.
Nucleic Acids Research 1-11 doi:10.1093/nar/gkp034