MitoFates
| Summary | MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position. |
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| Data type | protein - amino-acid sequence |
myPresto
| Summary | myPresto is a molecular simulation system for structure-guided molecular development. myPresto consists of about 50 programs and databases. Namely, molecular dynamics simulation for proteins/DNA, protein-compound docking software, in-silico screening programs, conformer generator, file converting tools, and etc.For in-silico screening, chemical compound database is necessary. The compound database is available from BIRC/AIST.You can down load myPresto without charge from the web site of MEDALS and Laboratory of Protein Informatics, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University. |
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| Data type | Protein-structure |
PAPIA
| Summary | Tools for protein information analyses such as similar structure search, Homologous sequence search and Multiple sequence search by PC cluster. |
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| Data type | Protein-structure |
PMID-Extractor
| Summary | PMID-Extractor allows a user to obtain PubMed IDs (PMIDs) from PDF files or text format files of journal paper in your hand. From Digital Object Identifiers (DOIs, http://en.wikipedia.org/wiki/Digital_object_identifier) or text information (e.g. titles) in the first page of each files, To start using PubMedScan, a paper recommender, PMIDs are required to specify the users' interest. That is the main usage of PMID-Extractor. |
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| Data type | Journal |
POODLE
| Summary | POODLE provides three types of disordered prediction according to length of the target disorder.POODLE-S and POODLE-L predict short disorder and long disorder regions,respectively. POODLE-W predicts which proteins are mostly disordered. |
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| Data type | Protein-AminoAcid |
PRRN
| Summary | PRRN is a multiple sequence alignment program by doubly nested randomized iterative method. PRRN accepts either nucleotide or protein sequences. PRRN repeatedly uses pairwise group-to-group alignment to improve the overall weighted sum-of-pairs score at each iterative step, where the pair weights are introduced to correct for uneven representations of the sequences to be aligned. The strategies of PRRN work most effectively for refining a crude alignment obtained by other more rapid methods, e.g. progressive alignment. (Summarized from the original site) |
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| Data type | DNA, amino acid sequences |
ScreenCap3
| Summary | Screening of caspase-3 substrates and cleavage site prediction |
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| Data type | protein - amino-acid sequence |
SlideSort
| Summary | SlideSort is fast and exact method that can find all similar pairs from a string pool in terms of edit distance (cited from the original site). |
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| Data type | DNA-sequence Protein-sequence |
SPALN
| Summary | Spaln is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. |
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| Data type | Comparative genomics |
TACT
| Summary | Transcriptome Auto-annotation Conducting Tool (TACT) is a web-based automated prediction tool of functional annotation that was developed by integrating ORF prediction, similarity search (BLASTX and FASTY) and motif prediction (InterProScan). TACT was produced in collaboration with the H-Invitational project, and has contributed to the development of the H-Invitational Database (H-InvDB). |
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| Data type | DNA-sequence |