S4: structure-based sequence alignments of SCOP superfamilies
نویسندگان
چکیده
منابع مشابه
S4: structure-based sequence alignments of SCOP superfamilies
S4 is an automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database. All structural domains that do not share more than 40% sequence identity as defined by the ASTRAL compendium of protein structures are included. The alignments are constructed using pairwise structural alignments to generate residue equivalences that are then ...
متن کاملPASS2: A Database of Structure-Based Sequence Alignments of Protein Structural Domain Superfamilies
Sequence alignments guided by structural features are particularly suited for distant relationships and they permit a better sampling of the protein sequence space. Reliable sequence alignments could be useful in evolutionary biology and in defining structurefunction relationships for protein superfamilies. PASS2 database presents structure-based alignments of protein domains related at the sup...
متن کاملSUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
The SUPERFAMILY database contains a library of hidden Markov models representing all proteins of known structure. The database is based on the SCOP 'superfamily' level of protein domain classification which groups together the most distantly related proteins which have a common evolutionary ancestor. There is a public server at http://supfam.org which provides three services: sequence searching...
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Accurate structure-based sequence alignments of distantly related proteins are crucial in gaining insight about protein domains that belong to a superfamily. The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. We thus report an automated, updated version of the superfamily alignment database known as PASS2.4, consis...
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MOTIVATION The Profile Neighbor Joining (PNJ) algorithm as implemented in the software ProfDist is computationally efficient in reconstructing very large trees. Besides the huge amount of sequence data the structure is important in RNA alignment analysis and phylogenetic reconstruction. RESULTS For this ProfDistS provides a phylogenetic workflow that uses individual RNA secondary structures i...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2004
ISSN: 1362-4962
DOI: 10.1093/nar/gki043