• PSI-BLAST

  • Referenced in 226 articles [sw17324]
  • BLAST: a new generation of protein database search programs. The BLAST programs are widely used ... tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety ... position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific...
  • Cd-hit

  • Referenced in 46 articles [sw16887]
  • popular sequence comparison and database search tools, such as BLAST. Availability:http://cd-hit.org...
  • BLAST

  • Referenced in 241 articles [sw17334]
  • Basic Local Alignment Search Tool. BLAST finds regions of similarity between biological sequences. The program ... compares nucleotide or protein sequences to sequence databases and calculates the statistical significance...
  • COCONUT

  • Referenced in 38 articles [sw04760]
  • Vienna Graph Template Library), and the search database is based on the VDBL (Vienna DataBaseLibrary ... scheme which proceeds by working on the search graph, a directed acyclic graph...
  • SIMPLIcity

  • Referenced in 86 articles [sw14893]
  • methods and narrowing down the searching range in a database. A measure for the overall...
  • NeTra

  • Referenced in 63 articles [sw14887]
  • NeTra: A toolbox for navigating large image databases. We present here an implementation of NeTra ... image regions to search and retrieve similar regions from the database. A distinguishing aspect ... algorithm that allows object- or region-based search. Image segmentation significantly improves the quality ... time of ingest into the database, and image attributes that represent each of these regions...
  • HMMER

  • Referenced in 17 articles [sw10514]
  • efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server ... implemented such that most protein database searches return within a few seconds. Methods are available ... searching either a single protein sequence, multiple protein sequence alignment or profile ... against a target sequence database, and for searching a protein sequence against Pfam...
  • VisualSEEk

  • Referenced in 89 articles [sw13846]
  • prototype system for searching by visual features in an image database. The VisualSEEk system...
  • SMART

  • Referenced in 16 articles [sw17187]
  • Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries...
  • MEME

  • Referenced in 14 articles [sw15711]
  • Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded ... sequences with databases of known motifs, search sequence databases for matches to the motifs...
  • MODELLER

  • Referenced in 33 articles [sw27731]
  • protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER...
  • SPADE

  • Referenced in 87 articles [sw02226]
  • existing solutions to this problem make repeated database scans, and use complex hash structures which ... search techniques, and using simple join operations. All sequences are discovered in only three database...
  • Chabot

  • Referenced in 39 articles [sw14898]
  • carefully chosen search criteria. We present an approach that integrates a relational database retrieval system ... goal was to integrate a relational database retrieval system with content analysis techniques that would ... method, if used in conjunction with other search criteria, improves our ability to retrieve images...
  • SSAHA

  • Referenced in 10 articles [sw17308]
  • SSAHA: a fast search method for large DNA databases. We describe an algorithm, SSAHA (SequenceSearch ... Alignment by HashingAlgorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences ... database are preprocessed by breaking them into consecutive k-tuples ofk contiguous bases and then ... each k-tuple. Searching for a query sequence in the database is done by obtaining...
  • RSEARCH

  • Referenced in 10 articles [sw23815]
  • been published that allow searching a sequence database for homologs of a single RNA molecule ... utilizes a local alignment algorithm to search a database for homologous RNAs. For this purpose ... which RSEARCH outperforms the primary sequence search programs BLAST and SSEARCH. The primary drawback...
  • GutenTag

  • Referenced in 5 articles [sw35329]
  • mass spectra of peptides has been database search software such as SEQUEST. A new sequence ... database search algorithm, called GutenTag, makes it possible to identify peptides with unknown posttranslational modifications ... spectrum and efficiently examines a sequence database for peptides that match these tags. When ... multiple candidate sequences result from the database search, the software evaluates which is the best...
  • JASPAR

  • Referenced in 40 articles [sw18502]
  • factors. The database is complemented by a web interface for browsing, searching and subset selection...
  • 01poly

  • Referenced in 16 articles [sw14281]
  • information is obtained by a search in a database generated by complete enumeration. For more...
  • FindStat

  • Referenced in 15 articles [sw13588]
  • database of combinatorial statistics and maps on combinatorial collections, and a search engine to identify ... provides a web interface to search and update the database, and as well a SageMath...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • computational advances in genome-scale RNA search create a need for tools for automatic, high ... that can be readily used for database search. Previous tools fall short of this goal...