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ALN
| Summary | Aln is a program for aligning a pair of nucleotide or amino acid sequences or alignments. Aln can even align a nucleotide sequence and a single or a group of protein sequences. This can be used to predict eukaryotic gene structures (protein-coding exons) based on sequence homology with known protein sequences. |
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| Data type | DNA, amino acid sequences |
ALNGG
| Summary | ALNGG detects the protein coding gene by genome comparison between two species. |
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| Data type | DNA-sequence , Genome |
ASIAN
| Summary | ASIAN is a tool for automatically inferring the relationships between objects from data including redundant information, e.g. expression profiles that were measured for a large number of genes under various conditions.The tool combines cluster analysis, regression analysis, and graphical Gaussian modeling.By inputting your raw data, you can obtain some relationships between objects: the correlation, the grouping, the group number, and the network graph. |
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| Data type | Gene expression profile |
CoCoozo
| Summary | CoCoozo is a search engine for analyzing MS spectrum data. CoCoozo performs parallelized high-speed database search with a set of MS spectrum data against existing protein sequence databases in order to identify proteins corresponding to the precursor ions from peak intensity patterns. |
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| Data type | Ptotein-sequence |
Data mining analysis of supersecondary structure
| Summary | The DCCP method (Dictionary of Conformational Code in Proteins) converts 3D information of protein X-ray crystal structure data to 1D information, and converts. Its conformation describe with only three kinds of codes into α helix pattern h, β sheet type pattern s, and other types pattern o. Especially useful for data mining of hyper-secondary structure like loop with complicated structure, it is useful for analysis of polymorphism of proteins with similar structures but amino acid sequences are very different. |
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| Data type | Protein structure |
DPClus
| Summary | DPClus is a graph clustering software, which makes it possible to detect and visualize clusters of proteins in interaction networks which mostly represent molecular biological functional units. |
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| Data type | Protein-function |
FORTE
| Summary | FORTE is a profile-profile comparison tool for protein fold recognition. Users can submit a protein sequence to explore the possibilities of structural similarity existing in known structures. Results are reported in the form of pairwise alignments. |
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| Data type | Protein-structure |
GPCRs Interaction Partners
| Summary | G-protein coupled receptor interaction partners (GRIP) is the web application to predict protein-protein interaction interfaces for G-protein coupled receptor oligomerization. This application provides predicted interfaces by Spatial Cluster Detection (SCD), Predicted interfaces are displayed interactively by using Jmol (cited from the original site). |
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| Data type | Interaction GPCR |
HEAT
| Summary | H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. This technique is called Gene Set Enrichment Analysis (GSEA), and is popularly used in analyzing results of microarray experiments. Fisher's exact probability is used in statistical tests of HEAT. |
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| Data type | Annotation |
HomeoRoq
| Summary | HomeoRoq allows us to quantify ratios of homeolog expression levels in allopolyploid species, and links to genome sequences and raw reads of A. halleri subsp. gemmifera and A. lyrata subsp. petraea.HomeoRoq is a pipeline to detect statistically significant changes in the homeolog-specific expression ratios under different conditions using RNA-seq data |
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| Data type | protein - amino-acid sequence |
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