The mission of UniProt is to provide the scientific community with a comprehensive, high quality and freely accessible resource of protein sequence and functional information. The site provides UniProtKB (protein knowledgebase) consisting of Swiss-Prot and TrEMBL sections; UniRef that speeds up sequence similarities search; and UniParc a squence archive.
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COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.
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Home Recent Results Saved Strategies Needleman-Wunsch Global Align Nucleotide Sequences
Category: Protein sequences alignment
The Needleman-Wunsch global alignment (now hosted by BLAST/NLM) performs a global alignment on two sequences. It is commonly used in bioinformatics to align protein or nucleotide sequences.
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Search protein databases with a protein query sequence to either identify the query sequence or find protein sequences similar to the query.Searches can be refined using algorythms available in the page: PSI-Blast, PHI-BLAST & DELTA-BLAST.
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PipeAlign2 is a protein family analysis tool integrating a multi-step process ranging from the search for sequence homologues in protein and 3D structure databases to the structural / functional annotation of the family. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated multiple sequence alignment (MSA) in which sequences are clustered into potential functional subgroups.
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DNA or genome alignment and visualization tool based on blastz alignment program. Alignments can be automatically submitted to rVista 2.0 to identify evolutionary conserved transcription factor binding sites.
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FOLDALIGN is an algorithm for local or global simultaneous folding and aligning two or more RNA sequences and is based on the Sankoffs algorithm (SIAM J. Appl. Math., 45:810-825, 1985). Foldalign can make pairwise local or global alignments and structure predictions. FoldalignM makes a multiple global alignment and structure prediction.
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MM-align is designed to structurally align multimeric protein complexes using heuristic iteration of dynamic programming based on TM-score rotation matrix. The multple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignment prevented. The alignment on interface structures can be enhenced by MM-align by an interface-specific weighting factor. A TM-score is reported for assessing the structural similarity of two complexes. Refere
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Engine for Protein Similarity Search. SSearch is optimal for short peptides, GGsearch is optimal to find sequences similar (>80%) in length to the guery sequence, GLsearch is fine to match a short sequence or domain to the full protein.
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TM-align is a computer algorithm for quick and accurate protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. References:Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm based on TM-score. Nucleic Acids Research, 2005 33: 2302-2309
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TM-score is an algorithm to calculate the topological similarity of two protein structures. It can be used to quantitatively access the quality of protein structure predictions relative to the native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive to the global topology of structures than the often-used root-mean-square deviation (RMSD). References: Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure temp
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NW-align is simple and robust alignment program for protein sequence-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. The mutation matrix is from BLOSUM62 with gap openning penaly=-11 and gap extension panalty=-1. The source code of this program can be downloaded at the bottom of the NW-align website, which can be easily modified for different purposes.
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