:: DESCRIPTION
MIDIA is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bowsher, C.G. (2011)
Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.
Bioinformatics (2011) 27 (4): 584-586.
:: DESCRIPTION
LIS alignment is a www interface for parsing BLAST output using the LIS (Longest Increasing Subsequence) algorithm. The softwar processes the BLAST result to find the longest consecutive list of HSPs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
No
:: MORE INFORMATION
Citation
Hongyu Zhang
Alignment of BLAST high-scoring segment pairs based on the longest increasing subsequence algorithm
BIOINFORMATICS Vol. 19 no. 11 2003, pages 1391–1396
:: DESCRIPTION
urms (unit-vector root mean squared) is a protein structure comparison program that compares two structures (in PDB format).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Golan Yona and Klara Kedem. (2005).
The URMS-RMS hybrid algorithm for fast and sensitive local protein structure alignment.
Journal of Computational Biology 12 12-32.
:: DESCRIPTION
prof_sim is a profile-profile comparison program that compares PSI-BLAST profiles.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Golan Yona and Michael Levitt.
Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. (2002).
Journal of Molecular Biology 315 1257-1275.
:: DESCRIPTION
SIB-BLAST (Simple Is Beautiful) is a novel algorithm developed to overcome the model corruption problem that occurs frequently in the later iterations of PSI-BLAST searches.The algorithm compares resultant hits from iteration two and the final iteration of a PSI-BLAST search, calculates the figure of merit for each “overlapped” hit and re-ranks the hits according to their figure of merit. The premise of the algorithm is based on the observation that the profile, namely, the position specific scoring matrix (PSSM), in the first two rounds of a PSI-BLAST search, is the least corrupted since it is comprised mostly of close homologs. These profiles are used to search for more distant homologs, which are used to generate subsequent PSSMs. As more distant homologs are incorporated into the PSSM, non-homologous sequences frequently get included also, thus leading to model corruption. Hence, “benchmarking” hits from later iteration against earlier round when the model is least corrupted should improve the accuracy of a PSI-BLAST search.
::DEVELOPER
Ralf Bundschuh‘s statistical physics group at the Department of Physics of The Ohio State University.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
M.M. Lee, M. Chan, and R. Bundschuh,
“Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches“,
Bioinformatics 24 (2008) 1339-1343.
:: DESCRIPTION
PTMClust is a software that can be applied to the output of blind PTM (Post-translational Modification) search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We showed that our technique outperforms two standard clustering algorithms on a simulated dataset. Additionally, we showed that our algorithm significantly improves sensitivity and specificity when applied to the output of three different blind PTM search engines, SIMS, InsPecT and MODmap. Additionally, PTMClust markedly outforms another PTM refinement algorithm, PTMFinder. We demonstrate that our technique is able to reduce false PTM assignments, improve overall detection coverage and facilitate novel PTM discovery, including terminus modifications. We applied our technique to a large-scale yeast MS/MS proteome profiling dataset and found numerous known and novel PTMs. Accurately identifying modifications in protein sequences is a critical first step for PTM profiling, and thus our approach may benefit routine proteomic analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Mar 15;27(6):797-806. Epub 2011 Jan 22.
Computational refinement of post-translational modifications predicted from tandem mass spectrometry.
Chung C, Liu J, Emili A, Frey BJ.
:: DESCRIPTION
The ISA (Iterative Signature Algorithm) was designed to reduce the complexity of very large sets of data by decomposing it into so-called “modules”. In the context of gene expression data these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different “resolutions” of the modular mapping. Since the ISA does not rely on the computation of correlation matrices (like many other tools), it is extremely fast even for very large datasets.
::DEVELOPER
Computational Biology Group ,Department of Medical Genetics, University of Lausanne
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.
Iterative signature algorithm for the analysis of large-scale gene expression data.
Bergmann S, Ihmels J, Barkai N.
:: DESCRIPTION
ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences) is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ABACAS: algorithm-based automatic contiguation of assembled sequences.
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M.
Bioinformatics. 2009 Aug 1;25(15):1968-9.
:: DESCRIPTION
The Kinwalker algorithm performs cotranscriptional folding of RNAs, starting at a user a specified structure (default: open chain) and ending at the minimum free energy structure. Folding events are performed between transcription of additional bases and are regulated by barrier heights between the source and target structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Mol Biol. 2008 May 23;379(1):160-73. Epub 2008 Mar 6.
Folding kinetics of large RNAs.
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C.
:: DESCRIPTION
NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
::DEVELOPER
Sérgio Anibal de Carvalho Junior
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
NeoBio is free software, so feel free to download and use it at your own will.