:: DESCRIPTION
PCOILS is a new COILS version that uses profiles as inputs
::DEVELOPER
Dept. of Protein Evolution at the Max Planck Institute for Developmental Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Struct Biol. 2006 Aug;155(2):140-5. Epub 2006 Mar 31.
Comparative analysis of coiled-coil prediction methods.
Gruber M, Soding J, Lupas AN.
:: DESCRIPTION
EDISA (Extended Dimension Iterative Signature Algorithm) is a novel probabilistic clustering approach for 3D gene-condition-time datasets. Based on mathematical definitions of gene expression modules, the EDISA samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality. We applied the algorithm to a synthetic dataset and were able to successfully recover the implanted modules over a range of background noise intensities.
::DEVELOPER
the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, Andreas Zell:
EDISA: extracting biclusters from multiple time-series of gene expression profiles
BMC Bioinformatics 2007, 8:334
:: DESCRIPTION
kernel-compute is a package that computes pairwise profile-based similarity matrix. This scoring matrix has shown to be the best performing method for developing remote homology detection and fold recognition models.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Huzefa Rangwala & George Karypis
Profile Based Direct Kernels for Remote Homology Detection and Fold Recognition
Bioinformatics 2005 21(23):4239-4247
:: DESCRIPTION
exim is a program that compares two time-series expression profiles using the dynamic programming algorithm. To avoid bias due to differences in magnitudes, the vectors are first normalized such that each has zero mean and standard deviation of one. Unlike sequence comparison, gaps are not allowed, since the meaning of a gap is that a time delay is introduced. If two genes are co-expressed (possibly with a time-shift) it is unlikely that one will re-synchronize itself to the other, once they departed (a gap was introduced).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PCMA constructs a multiple sequence alignment given a set of protein sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J.Pei, R.I.Sadreyev, and N.V.Grishin (2003)
“PCMA: Fast and Accurate Multiple Sequence Alignment Based on Profile Consistency“.
Bioinformatics 19(3): 427-428.
:: DESCRIPTION
HangOut is a software for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
B.H. Kim, Q. Cong, N.V. Grishin (2010)
“HangOut: generating clean PSI-BLAST profiles for domains containing long insertions“.
Bioinformatics (2010) 26 (12): 1564-1565.
:: DESCRIPTION
Prf browser is the program to plot expression profiles and to browse Peak-mapper, Event-mapper data, profiles for extracted genes from directory “genes” created by Glob-mapper or profiles by the unique gene identifiers (i.e. d2378). Prf-browser requires profile data (*.rsz or *aln) and the ID file with gene names as well.
::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
DynBin is a dynamic programming algorithm based binning method for ARISA data analysis which minimizes the overall differences between replicates from the same sampling spot. Data preprocessing identifies several outliers which are later found to be due to systematic errors. Clustering analysis of the time spots based on the binned data reveals important features of the biodiversity of the microbial communities.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun (2006),
A Dynamic Programming Algorithm for Binning Microbial Community Profiles.
Bioinformatics 22:1508-1514
:: DESCRIPTION
Treephyler is a tool for fast taxonomic profiling of metagenomes. It combines the predictive power of tree-based and speed of signature-based approaches. Treephyler was evaluated on a real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling.
::DEVELOPER
Department of Bioinformatics , University of Göttingen
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
F. Schreiber, P. Gumrich , R. Daniel and P. Meinicke (2010)
Treephyler: fast taxonomic profiling of metagenomes
Bioinformatics 26, 960-961
