• BLAST

  • Referenced in 251 articles [sw17334]
  • BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences...
  • PSI-BLAST

  • Referenced in 235 articles [sw17324]
  • searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional ... much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • protein sequences. With the avalanche of biological sequences generated in the post-genomic ... effectively formulate the sequence of a biological sample (such as DNA, RNA or protein) with ... difficult for users to formulate the biological sequences according to their desired features or properties ... computational proteomics, genomics, as well as biological sequence analysis. Moreover, to maximize users’ convenience...
  • TEIRESIAS

  • Referenced in 16 articles [sw35978]
  • Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. MOTIVATION: The discovery of motifs ... biological sequences is an important problem. RESULTS: This paper presents a new algorithm ... discovery of rigid patterns (motifs) in biological sequences. Our method is combinatorial in nature...
  • 2D-MH

  • Referenced in 21 articles [sw19727]
  • server for generating graphic representation of protein sequences based on the physicochemical properties of their ... acids. Introduction of graphic representation for biological sequences can provide intuitive overall pictures as well...
  • MEME

  • Referenced in 13 articles [sw15711]
  • MEME: discovering and analyzing DNA and protein sequence motifs. MEME (Multiple EM for Motif Elicitation ... novel ‘signals’ in sets of biological sequences. Applications include the discovery of new transcription factor ... find new sequence patterns in biological sequences and analyze their significance...
  • Memtype-2L

  • Referenced in 39 articles [sw16472]
  • through pse-PSSM. Given an uncharacterized protein sequence, how can we identify whether ... because they are closely relevant to the biological function of the query protein ... molecules in a biological system. Particularly, with the avalanche of protein sequences generated...
  • iRNA-PseColl

  • Referenced in 31 articles [sw24441]
  • sequence is a key for in-depth understanding of their biological functions and mechanism. Unfortunately ... individual and collective features of the sequence elements into the general pseudo K-tuple nucleotide...
  • INDELible

  • Referenced in 8 articles [sw23043]
  • INDELible: a flexible simulator of biological sequence evolution. Many methods exist for reconstructing phylogenies from...
  • FASTA3

  • Referenced in 7 articles [sw15724]
  • Flexible sequence similarity searching with the FASTA3 program package. Since the publication ... first rapid method for comparing biological sequences 15 years ago (1), DNA and protein sequence...
  • uShuffle

  • Referenced in 4 articles [sw26135]
  • uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts. Background ... evaluate the statistical significance of a biological sequence. In many cases, biologists need sophisticated shuffling ... generating uniform random permutations of biological sequences (such as DNAs, RNAs, and proteins) that preserve...
  • PANOW

  • Referenced in 7 articles [sw10156]
  • search of rare words in biological sequences (over- or under-represented words...
  • SeqinR

  • Referenced in 4 articles [sw08300]
  • seqinr: Biological Sequences Retrieval and Analysis. Exploratory data analysis and data visualization for biological sequence...
  • Biostrings

  • Referenced in 4 articles [sw14509]
  • Bioconductor package. String objects representing biological sequences, and matching algorithms. Memory efficient string containers, string ... utilities, for fast manipulation of large biological sequences or sets of sequences...
  • Pse-analysis

  • Referenced in 6 articles [sw23361]
  • Python package for DNA/RNA and protein/peptide sequence analysis based on pseudo components and kernel methods ... benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset...
  • MADMX

  • Referenced in 6 articles [sw35273]
  • including don’t care characters, from biological sequences. We introduce density, a simple and flexible...
  • iSNO-AAPair

  • Referenced in 24 articles [sw22447]
  • sites purely based on biological experiments. Facing the explosive protein sequence data generated...
  • LSTM

  • Referenced in 37 articles [sw03373]
  • output sequences, with or without a teacher. They are computationally more powerful and biologically more ... analysis, stock market prediction, and many other sequence problems...
  • BioRuby

  • Referenced in 5 articles [sw21661]
  • parsed to extract information you need. Biological sequences can be treated with the fulfilling methods ... Hmmer and many other softwares for the biological analysis can be executed within the BioRuby...
  • ESMERALDA

  • Referenced in 5 articles [sw25968]
  • operating on sequential data (speech, handwriting, biological sequences). It supports continuous density Hidden Markov models...