2013年2月13日星期三

Softberry programs for genomics

Softberry Programs available to academic users at no charge for occasional use in research projects
Program nameHelpDocumentationLinuxMac/Windows (W)Results ViewerTitle
ReadsMapViewDownloadDownloadDownloadReads Mapping ViewerMapping of reads to chromosome (contig)
Reads Mapping ViewerViewDownloadDownloadDownloadThe "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data.
AssemblerViewDownloadDownloadDownloadAssember ViewerAlgorithm of ab initio genome assembling using data produced by next-generation sequencing machines (Illumina/Solexa/etc). To view the program output data the Assembler Viewer can be used.
Assembler ViewerViewDownloadDownloadDownloadThe "Assembler Viewer" software is developed to visualize the "Assembler" output data.
SNP-ToolboxViewDownloadDownload (4.3Gb)Download  (W) (3.8GB)A fast and effective tool for analysis of genome variations in human chromosomes.
Promoter
CPGFinderViewDownloadDownloadDownloadSearch for CpG islands in sequences
FPROMViewDownloadDownloadDownloadHuman promoter prediction
NsiteViewDownloadDownloadDownloadSearch for of consensus patterns with statistical estimation.
Nsite-mViewDownloadDownloadDownloadSearch for regulatory motifs conserved in several sequences
PatternViewDownloadDownloadDownloadSearch for significant patterns in the set of sequences.
PolyahViewDownloadDownloadDownloadRecognition of 3'-end cleavage and polyadenilation region
ScanWM-PLViewDownloadDownloadDownloadSearch for weight matrix patterns of plant regulatory sequences
TSSGViewDownloadDownloadDownloadRecognition of human PolII promoter region and start of transcription
Protein Structure
3D-CompViewDownloadDownloadDownload3D-ExplorerSequence Alignment to Superposition
3D-MatchViewDownloadDownloadDownload3D-ExplorerPairwise protein structure alignment
3D-ModelFitViewDownloadDownloadDownload3D-ExplorerProgram for the estimation of quality of 3D model structure of protein.
Abini3DViewDownloadDownloadDownload3D-ExplorerAb inition folding
CysRecViewDownloadDownloadDownloadPrediction of SS-bonding states of cysteines and disulphide bridges in protein sequences
GetAtomsViewDownloadDownloadDownload3D-ExplorerOptimization of replaced side chain groups by simulated annealing algorithm
MolDynViewDownloadDownloadDownload3D-ExplorerMolDyn is designed to perform multiple tasks with protein structure.
MolMechViewDownloadDownloadDownload3D-ExplorerEnergy minimization program by molecular mechanic
NNSSPViewDownloadDownloadDownloadNearest-neighbor SS prediction
Net-SSPredictViewDownloadDownloadDownloadProgram for secondary structure prediction. Neural nets based on profile of psiBLAST comparison of the query sequence with NR database.
PDisorderViewDownloadDownloadDownloadProgram for predicting ordered and disordered regions in protein sequences
SSEnvIDViewDownloadDownloadDownloadProtein secondary structure and environment assignment from atomic coordinates
SSPViewDownloadDownloadDownloadPrediction of a-helix and b-strand segments of globular proteins
SSPALViewDownloadDownloadDownloadPrediction of protein secondary sturcture by using local alignments
Alignments
ProtmapViewDownloadDownloadDownloadMapping of a set of proteins on genome
MaliNViewDownloadDownloadDownloadMaliN ViewerMultiple alignment for nucleotide sequences.
MaliPViewDownloadDownloadDownloadMaliP ViewerMultiple alignment for protein sequences.
EstMapViewDownloadDownloadDownloadProgram for mapping a whole set of mRNAs/ESTs to a chromosome sequence
Scan2ViewDownloadDownloadDownloadProgram for aligning two multimegabyte-size genome sequences using a sequential search for most significant similarity regions.
Scan2aViewDownloadDownloadDownloadProgram for aligning two aminoacid sequences using a sequential search for most significant similarity regions.
Gene Finding
FexViewDownloadDownloadDownloadPrediction of internal, 5'- and 3'- exons in Human DNA sequences.
FgenesViewDownloadDownloadDownloadSequence Explorer,PDFGenesPattern based human gene structure prediction (multiple genes, both chains).
Fgenes-mViewDownloadDownloadDownloadSequence Explorer,PDFGenesPattern-based prediction of multiple variants of gene structure
FspliceViewDownloadDownloadDownloadProgram provides the possibility to search for both donor and acceptor sites, and to define thresholds for them independently. Program allows to search minor variants of splicing donor site (GC-site) as well.
PDFGenesViewDownloadDownloadDownloadPDFGenes utilizes the results of Gene Finding software, such as FGenesh, FGenesh+,FGenesh-C, FGenesh-2, FGenes, FGenes-mand BestORF, and represents them in PDF format for better viewability.
PSFViewDownloadDownloadDownloadFinding pseudogenes in a genomic sequence.
RnasplViewDownloadDownloadDownloadProgram for predicting exon-exon junction positions in cDNA sequences. For this program gcc fortran library should be installed locally.
SPLViewDownloadDownloadDownloadPrediction of splice sites in DNA sequences. For this program gcc fortran library should be installed locally.
SplMViewDownloadDownloadDownloadPrediction of splice sites in Human DNA sequences.
Bacterial Gene Finding
ABSplitViewDownloadDownloadDownloadSequence ExplorerProgram determines for the nucleotide sequence of approx. 300-600 n.p. whether it belongs to archeal or bacterial genome.
BpromViewDownloadDownloadDownloadPrediction of bacterial promoters
FindTermViewDownloadDownloadDownloadRNA Secondary Structure ViewerSearchs for bacterial terminators in DNA sequences.
RNA Strucuture
Bestpal-EViewDownloadDownloadDownloadCalculates best palindrome for given RNA sequence, and also a set suboptimal palindromes (sorted by energy)
Bestpal-HViewDownloadDownloadDownloadRNA Secondary Structure ViewerCalculates best palindrome for given RNA sequence with restrictions.
Bestpal-WViewDownloadDownloadDownloadRNA Secondary Structure ViewerProgram for searching best "linear" RNA secondary structure for long sequences with a window moving along the sequence.
Find-miRNAViewDownloadDownloadDownloadSearchs for pre-miRNAs in a given RNA sequence and for miRNA in each found pre-miRNA.
FoldRNAViewDownloadDownloadDownloadRNA Secondary Structure ViewerProgram for RNA secondary structure prediction based on dynamic programming (Nussinov and Jackonson, 1978, Zuker, 2005).
Protein Location
PSiteViewDownloadDownloadDownloadSearch for of prosite patterns with statistical estimation.
CTL-EpitopeViewDownloadDownloadDownloadThis program is designed for prediction of CTL epitopes of length=9 in protein sequences.
Protcomp-ANViewDownloadDownloadDownloadProgram for Identification of sub-cellular localization of Eukaryotic proteins: Animal/Fungi.
Protcomp-BViewDownloadDownloadDownloadProgram for Identification of sub-cellular localization of bacterial proteins.
Protcomp-PLViewDownloadDownloadDownloadProgram for Identification of sub-cellular localization of Eukaryotic proteins: Plants
Repeats
LCRepViewDownloadDownloadDownloadSequence ExplorerProgram for mapping low complexity regions in nucleotide sequences.
LCRep-PViewDownloadDownloadDownloadSequence ExplorerProgram for mapping low complexity regions in protein sequences.
TandemRepViewDownloadDownloadDownloadProgram for mapping the Tandem Repeats Regions in nucleotide sequences.
TandemRep-PViewDownloadDownloadDownloadProgram for mapping the Tandem Repeats Regions in protein sequences.
SelTag
BdClustViewDownloadDownloadDownloadClustering of gene expression profiles or samples by Ben-Dor algorithm.
CHPImportViewDownloadDownloadDownloadImport expression data from the Affymetrix CHP format to SelTag data file.
FieldCorrViewDownloadDownloadDownloadGraph ViewerThe program calculates correlation coefficients between the gene expression values in experiments (fields).
GeneCorrViewDownloadDownloadDownloadGraph ViewerThe program calculates correlation coefficients between the gene expression profiles.
HClustViewDownloadDownloadDownloadClustering of gene expression profiles by hierarchical algorithm.
Mas5NormViewDownloadDownloadDownloadNormalization of the Affymetrix gene expression row data by MAS 5.0 algorithm.
Mas5BaselineViewDownloadDownloadDownloadComparison of the Affymetrix gene expression row data to the baseline data by MAS 5.0 algorithm.
SelByExprViewDownloadDownloadDownloadGene selection by query (logical expression).
SelCorrViewDownloadDownloadDownloadGraph ViewerThe program selects most correlated genes for specified gene set.
SOMClustViewDownloadDownloadDownloadThe program clusters gene expression profiles or samples by SOM (Self-Organizing Map) algorithm.
Statistics
SNNBP-LearnViewDownloadDownloadDownloadSNNBP-Learn implement the back-propagation training algorithm and output the optimal NN structure, saved in the SNNBP internal format.
SNNBP-PredictViewDownloadDownloadDownloadSNNBP-Predict - neural network calculate output values (predictions) using input values from the data file (target values need not be specified in this option).
SNNBP-TestViewDownloadDownloadDownloadSNNBP-Test implement testing of the previously obtained network on the user data.
Seqman
RestrictaseViewDownloadDownloadDownloadRestrictase ViewerThe program for finding and displaying the positions of the cut sites of restriction enzyme recognition sequences.
Viewers
3D-ExplorerViewDownloadDownloadDownload3D Explorer is designed to visualize spatial models of biological macromolecules and their complexes. Application is compatible with PDB files.
Assembler ViewerViewDownloadDownloadDownloadThe "Assembler Viewer" software is developed to visualize the "Assembler" output data.
DotPlot viewerViewDownloadDownloadDownloadDotPlot viewer provides the possibility to visualize the sites of homology between the sets of sequences.
GraphViewDownloadDownloadDownloadThe application is made for visualization of statistics files.
MaliN ViewerViewDownloadDownloadThe "MaliN viewer" application is developed for aligning nucleotide sequences and working with results of such alignments.
MaliP ViewerViewDownloadDownloadThe "MaliP viewer" application is developed for aligning protein sequences and working with results of such alignments.
Reads Mapping ViewerViewDownloadDownloadDownloadThe "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data.
Restrictase ViewerViewDownloadDownloadDownloadThe "Restrictase viewer" application is purposed for visualization of restriction sites that were found with use of "Restrictase" program.
RNA Secondary Structure ViewerViewDownloadDownloadDownloadRNA Secondary Structure Viewer is made for visualization and manipulation of RNA secondary structure.
Sequence ExplorerViewDownloadDownloadDownloadSequence Explorer provides the visual representation of genome annotations.
Posted by at
Labels: , ,

没有评论:

发表评论

订阅： 博文评论 (Atom)