• Arlequin

  • Referenced in 5 articles [sw11442]
  • instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like...
  • MUMMER

  • Referenced in 40 articles [sw17256]
  • fast alignment of large-scale DNA and protein sequences. MUMmer is a system for rapidly ... easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will ... species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • sequence of a biological sample (such as DNA, RNA or protein) with a discrete model ... vector that can effectively reflect its sequence pattern information or capture its key features concerned ... problem, all these tools, however, can only handle one type of samples. Furthermore, the number ... difficult for users to formulate the biological sequences according to their desired features or properties...
  • PGEToolbox

  • Referenced in 1 article [sw12455]
  • follows: 1) capability for handling both DNA sequence polymorphisms and single nucleotide polymorphisms (SNPs), which...
  • DV-Curve

  • Referenced in 6 articles [sw35268]
  • find graphic tools to study DNA sequence in a perceivable form. A large number ... this field. However, it is difficult to handle the following problems in one graph ... difficulty of visualization when representing long DNA sequences and (v) need to reflect useful information...
  • PASS

  • Referenced in 3 articles [sw35276]
  • reference DNA, typically a genomic sequence. It is designed to handle a huge amount...
  • RRBSMAP

  • Referenced in 2 articles [sw23509]
  • selection, resulting in DNA sequencing data that require special bioinformatic handling. Here, we describe RRBSMAP...
  • spgs

  • Referenced in 1 article [sw41881]
  • Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects...
  • BSmooth

  • Referenced in 11 articles [sw23483]
  • bisulfite sequencing reads to differentially methylated regions. DNA methylation is an important epigenetic modification involved ... measured using whole-genome bisulfite sequencing. However, cost, complexity of the data, and lack ... results even with low coverage data, appropriately handling biological replicates. BSmooth is open source software...
  • Phrap

  • Referenced in 5 articles [sw18792]
  • program for assembling shotgun DNA sequence data. Among other features, it allows ... presence of repeats, it constructs the contig sequence as a mosaic of the highest quality ... trouble-shooting assembly problems, and it handles large datasets. See the phrap/cross_match/swat documentation and phrap...
  • ACME

  • Referenced in 1 article [sw29727]
  • magnitude longer sequences (e.g., DNA for the entire human genome); handles large alphabets (e.g., English...
  • Regexpcount

  • Referenced in 6 articles [sw00792]
  • which may be constrained. This extension also handles matches with errors. The package is fully ... genome (a Markovian sequence), knowing that an (overrepresented DNA protecting) pattern named Chi occurs...
  • Consed

  • Referenced in 2 articles [sw18793]
  • sequencing. Summary: The rapid growth of DNA sequencing throughput in recent years implies that graphical ... viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions...
  • CANADA

  • Referenced in 1 article [sw21675]
  • DNA sequences that meet these and other requirements, as well as for analyzing and handling...
  • Repseek

  • Referenced in 3 articles [sw13190]
  • detecting all approximate repeats in DNA sequences allowing for gaps and a substitution matrix ... method is computationally efficient enough to handle large sequences and is flexible enough to account...
  • GSNAP

  • Referenced in 1 article [sw17306]
  • GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality. The programs ... DNA-Seq datasets to genomes, have evolved along with advances in biological methodology to handle ... include linear genomes that can compare sequences using single-instruction multiple-data (SIMD) instructions, compressed...
  • Pandoo

  • Referenced in 1 article [sw38148]
  • exploring and characterising bacterial whole genome DNA sequence data. It is a computational pipeline written ... implementation using the ruffus pipeline library. Ruffus handles task-scheduling and task-parallelisation during...
  • pyLEMMINGS

  • Referenced in 1 article [sw22398]
  • experimentally annotating properties of proteins and DNA sequences. Standard supervised learning algorithms assume accurate instance ... Multiple instance learning is a paradigm for handling such labeling ambiguities. However, the widely used...
  • 3DNA

  • Referenced in 4 articles [sw21991]
  • Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded ... complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify ... diffraction measurements of various repeating sequences can also be generated within the program...
  • RepeatAssembler

  • Referenced in 1 article [sw13669]
  • identification of full-length consensus sequences for repetitive DNA fragments or the genetic material that ... fall-length repeats is particularly intricate and handling this task properly is both the goal ... solution. REPEATASSEMBLER analyzes as few sequences as possible to screen out all repetitive sequences. Then...