:: DESCRIPTION
PROBCONS is an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005.
PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment.
Genome Research 15: 330-340.
:: DESCRIPTION
RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rasmus Wernersson and Anders Gorm Pedersen.
RevTrans – Constructing alignments of coding DNA from aligned amino acid sequences.
Nucl. Acids Res., 2003, 31(13), 3537-3539.
:: DESCRIPTION
SARpred, a neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment. In this method, two feed forward, back-propagation networks are used. The first sequence-to-structure network is trained with PSI-BLAST generated position specific scoring matrices. Further, the initial predictions from the first network and PSIPRED predicted secondary structure are used as input to the second structure-to-structure network. The input is a single letter-code amino acid sequence in free format and output is a real value of surface accessiblity corresponding to the amino acid sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Garg A, Kaur H & Raghava GP. (2005).
Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure information.
Proteins. 61: 318-24
:: DESCRIPTION
LGEpred allows user to analsis the expresion data (Microarray Data) where it calculate correlation coefficient between amino acid residue and gene expression level.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Raghava, G. P. S. and Han, J. H. (2005)
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein.
BMC Bioinformatics 6:59.
:: DESCRIPTION
SequenceAssembly is a program to assemble amino acid sequences of entire proteins
::DEVELOPER
The Mass Spectrometry Laboratory
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GeneSilico MetaDisorder web service provides access to metapredictor designed to predict disorder in proteins using existing bioinformatics tools and machine learning.For final consensus 15 other protein disorder tools (DisEMBL, IUPred, DISPORED, etc.) and 8 fold recognition methods (HHsearch, mGenThreader, etc.) are used.Method was carefully benchmarked and validated using our own dataset and during blind tests CASP8 and CASP9, always showing superirority in comparision to methods.
::DEVELOPER
Lukasz Kozlowski from Laboratory of Bioinformatics and Protein Engineering at The International Institute of Molecular and Cell Biology in Warsawa
:: SCREENSHOTS
:: REQUIREMENTS
no (only web service)
:: MORE INFORMATION
Citation
Kozlowski LP, Bujnicki JM.
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins.
BMC Bioinformatics. 2012 May 24;13(1):111.
:: DESCRIPTION
IQPNNI (Important Quartet Puzzling and NNI Operation) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees. The key ingredient is the definition of so-called important quartets (IQs), which allow the computation of an intermediate tree in O(n^2) time for n sequences. The resulting tree is then further optimized by applying the nearest neighbor interchange (NNI) operation. Subsequently a random fraction of the sequences is deleted from the best tree found so far. The deleted sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Le Sy Vinh and Arndt von Haeseler (2004)
IQPNNI: Moving fast through tree space and stopping in time.
Mol. Biol. Evol., 21(8):1565-1571.