:: DESCRIPTION
fLPS is a package for the annotation of Compositional Biases (CB) regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Harrison PM.
fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences.
PeerJ. 2021 Oct 28;9:e12363. doi: 10.7717/peerj.12363. PMID: 34760378; PMCID: PMC8557692.
:: DESCRIPTION
BiSSAP is a computer program designed to facilitate the creation of sequence listings for patent applications containing biological sequences (see Rule 30 EPC, Rule 5.2 PCT, and the Decision of the President and Notice from the EPO dated 28 April 2011 (OJ EPO 6/2011, 372 ff.)).
::DEVELOPER
EPO BiSSAP Team (bissap@epo.org)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
EFFECT is an algorithmic framework for automated detection of functional signals in biological sequences.
::DEVELOPER
Computational Biology lab, George Mason University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kamath U, De Jong K, Shehu A.
Effective automated feature construction and selection for classification of biological sequences.
PLoS One. 2014 Jul 17;9(7):e99982. doi: 10.1371/journal.pone.0099982. PMID: 25033270; PMCID: PMC4102475.
:: DESCRIPTION
LogOddsLogo is a web based application designed to make the generation of sequence logos from biological sequence alignments simple.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
Log-Odds Sequence Logos.
Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF.
Bioinformatics. 2014 Oct 6. pii: btu634
:: DESCRIPTION
BioSAVE is a program for visualising DNA or protein sequences and annotations thereof. Annotations is used in a very broad sense here, encompassing any annotation that may be expressed in GFF format.
::DEVELOPER
Richard Pollock and Boris Adryan
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2008 Mar 20;9:157. doi: 10.1186/1471-2105-9-157.
BioSAVE: display of scored annotation within a sequence context.
Pollock RF1, Adryan B.
:: DESCRIPTION
BIAS: a novel sensitive method for the detection of user-defined compositional bias in biological sequences.
BIAS automatically searches a user-supplied protein sequence for segments that contain unusually dense clusters of user-specified amino acid types and computes analytical estimates of the statistical significance of each cluster. These estimates are based on the discrete scan statistics that allows one to detect segments that exhibit even subtle local deviations from the random independence model.
ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
I.Kuznetsov and S.Hwang (2006)
A novel sensitive method for the detection of user-defined compositional bias in biological sequences.
Bioinformatics, 22(9):1055-1063
I.Kuznetsov (2008)
ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
Bioinformatics 24(13): 1534-1535
:: DESCRIPTION
BATS consists of a collection of libraries that can be used to run basic sequence analysis tasks. Routines for global alignment (LCS from Fragments, Edit Distance with Gaps), local alignment (approximata string matching with K mismateches or differences), and statistical analysis (Filter, Z-Score and Model Generation ) are included.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Algorithms Mol Biol. 2007 Sep 18;2:10.
A basic analysis toolkit for biological sequences.
Giancarlo R1, Siragusa A, Siragusa E, Utro F.
:: DESCRIPTION
Kolmogorov is a multistep approach to classify and cluster Biological Sequences and Structures, via Compression.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2007 Jul 13;8:252.
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
Ferragina P1, Giancarlo R, Greco V, Manzini G, Valiente G.
:: DESCRIPTION
Jstacs is an open source Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches for parameter learning. Using Jstacs, classifiers can be assessed and compared on test datasets or by cross-validation experiments evaluating several performance measures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Michael Seifert, Marc Strickert, Alexander Schliep and Ivo Grosse
Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models
Bioinformatics (2011) 27 (12): 1645-1652.
:: DESCRIPTION
The seqinR package for the R environment is a library of utilities to retrieve and analyse biological sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
D. Charif, J. Thioulouse, J. R. Lobry and G. Perrière
Online synonymous codon usage analyses with the ade4 and seqinR packages
Bioinformatics (2005) 21 (4): 545-547
