• STAR

  • Referenced in 9 articles [sw35644]
  • method named STAR, identifies all segments of the sequence that correspond to significant approximate tandem ... description length criterion to identify which sequence segments are ATR. Our optimization procedure guarantees that...
  • ELM

  • Referenced in 8 articles [sw17021]
  • proteomes. Individual functions assigned to different sequence segments combine to create a complex function ... available for revealing globular domains in sequences, there has hitherto been no comprehensive collection...
  • GlobPlot

  • Referenced in 7 articles [sw06213]
  • partially or wholly unstructured. Non-globular sequence segments often contain short linear peptide motifs...
  • PipMaker

  • Referenced in 8 articles [sw17257]
  • comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution ... which shows both the position in one sequence and the degree ... similarity for each aligning segment between the two sequences in a compact and easily understandable ... plot of the locations of those segments in both species (similar to a dot plot...
  • breakfast

  • Referenced in 6 articles [sw22395]
  • point detection in data sequences, or sequence segmentation, using computationally efficient multiscale methods. This version...
  • MAVG

  • Referenced in 9 articles [sw10918]
  • locating non-overlapping maximum average segments in a given sequence. Summary: MAVG is a software ... overlapping maximum-average segments that are sufficiently long in a given sequence of real numbers...
  • SEGID

  • Referenced in 9 articles [sw35743]
  • SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments. Summary: SEGID is a tool for finding...
  • HybridNET

  • Referenced in 3 articles [sw14682]
  • high confidence by looking at a segment of sequences or a set of genes. When ... looking at another segment of sequences, a different phylogenetic tree can be obtained with high...
  • Mauve

  • Referenced in 16 articles [sw24606]
  • transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently...
  • DIALIGN-TX

  • Referenced in 7 articles [sw12751]
  • greedy and progressive approaches for segment-based multiple sequence alignment. Background: DIALIGN...
  • GeneFizz

  • Referenced in 3 articles [sw10919]
  • genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives ... comparison between two types of segmentations for DNA sequences (possibly annotated): the coding/non-coding segmentation associated...
  • SS-Wrapper

  • Referenced in 2 articles [sw30878]
  • identify statistically significant matches between newly sequenced segments of genetic material and those in databases ... light of the rapid growth of biological sequence databases due to the emergence of high ... throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even ... utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications...
  • LEON

  • Referenced in 2 articles [sw24616]
  • detection of compositionally biased sequence segments. The accuracy and reliability of the predictions is demonstrated ... large-scale comparisons with structural and sequence family databases, where the specificity was shown...
  • ANNIE

  • Referenced in 2 articles [sw17016]
  • overview of possible functional assignments of sequence segments in the query proteins. The results ... integrated manner using an innovative AJAX-based sequence viewer. ANNIE is available online...
  • Sarment

  • Referenced in 2 articles [sw29814]
  • object-oriented Python modules for sequence segmentation via HMM analysis and Maximal Predictive Partitioning. Sarment ... data classes to store data such as sequences and vectors, count classes to compute counts...
  • dissectHMMER

  • Referenced in 1 article [sw17018]
  • framework that statistically evaluates fold-critical sequence segments for domain fold similarity. dissectHMMER: a HMMER ... framework that statistically evaluates fold critical sequence segments for domain fold similarity; a pragmatic step ... generalized into three stages: 1) sequence to domain alignment generation (hmmpfam/hmmscan against Pfam release...
  • Seglearn

  • Referenced in 6 articles [sw23641]
  • learning time series or sequences using a sliding window segmentation approach. The implementation provides ... classification, regression, and forecasting problems with multivariate sequence and contextual data. This package is compatible...
  • AutoMotif

  • Referenced in 4 articles [sw35529]
  • local sequence information. The local sequence preferences of short segments around PTM residues are described...
  • PyClone

  • Referenced in 9 articles [sw26928]
  • clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while ... introduced by segmental copy-number changes and normal-cell contamination. Single-cell sequencing validation demonstrates...
  • V-Xtractor

  • Referenced in 1 article [sw33186]
  • locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal...