Computational Framework for Biotechnological Research

Annotation

Annotation software system design to find the genes (places in the DNA sequence that encode a protein), the transfer RNA, and other features, and to make initial assignments of function to those genes.

Software Name Description
Synteny Synteny compares two genomes with each other using the famous mummer software package. The DNA sequences are first compared at the DNA level using Nucmer
Artemis DNA Sequence Viewer and Annotation Tool that allows visualisation of sequence features and the results of analyses within the context of the sequence, and also its six-frame translation.
Protein Finder Protein finder is a gendetector. The program finds genes by performing blastx searches of the input sequence against non redundant database.
Glimmer Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
GlimmerHMM GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).
tRNAscan The program identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
Boxer Boxer searches for Box Elements in genomic DNA. Box elements are a certain type of repeat region that only occurs in few species.
FingerPRINTScan FingerPRINTScan is a tool that classifies sequences using the family definitions that are present in the PRINTS database. It is particularly good at detecting distant evolutionary relationships.
Inquisitor The Inquisitor examines input protein sequence and identify whether or not it corresponds to a sequence in Integr8 (complete proteomes only) and the UniProt Knowledgebase.
InterProScan The InterPro database integrates PROSITE , PRINTS, Pfam, ProDom, SMART, TIGRFAMs, PIR superfamily, SUPERFAMILY Gene3D, PANTHER and HAMAP databases. InterPro data is distributed in XML format and it is freely available under the InterPro Consortium copyright.
Phobius This server is for prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.
PPSearch This server searches query sequence for protein motifs, rapidly compare query protein sequence against all patterns. stored in the PROSITE pattern database and determine what the function of an uncharacterised protein is.
Pratt This tool allows the user to search for patterns conserved in sets of unaligned protein sequences.
Radar RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. Radar is used as an automatic algorithm, for segmenting your query sequence into repeats, it identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in your query sequence.
Proteax Proteax software suite is used to handle modified proteins and protein derivatives.

 
 
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