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3D structure protein databases, Protein sequence databases MobiDB: Database of intrinsically disordered and mobile proteins: John Moult, Christine Orengo, Predrag Radivojac University of Padua: Italian Government database of intrinsic protein disorder annotation 3D structure protein databases, Protein sequence databases ModBase
an algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. 2: Yes: Yes: No: sourcecode Archived 2008-02-11 at the Wayback Machine [56] [57] [58] Foldalign
BLAST's nucleotide alignment program, slow and not accurate for short reads, and uses a sequence database (EST, Sanger sequence) rather than a reference genome. BLAT: Made by Jim Kent. Can handle one mismatch in initial alignment step. Yes, client-server Proprietary, freeware for academic and noncommercial use [36] 2002 Bowtie
The ARB Project is a free software package for the phylogenetic analysis of rRNA and other biological sequences including DNA and protein sequence. It simplifies the import and assembly of genetic sequences from any organisms with the use of an automated aligner.
SimTandem is a database search engine for identification of peptide sequences from LC/MS/MS data. The engine can be used as an external tool in OpenMS/TOPP. [23] SQID Open source: SeQuence IDentification (SQID) is an intensity-incorporated protein identification algorithm for tandem mass spectrometry. Tide (rewrite of Crux) Open source
Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms, GENSCAN server is the GenomeScan's predecessor: Vertebrate, Arabidopsis, Maize [24] GENSCAN: Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms: Vertebrate, Arabidopsis, Maize [25 ...
The Reference Sequence (RefSeq) database [1] is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was introduced in 2000.