• ScalaBLAST

  • Referenced in 7 articles [sw08812]
  • High-Performance Data-Intensive Bioinformatics Analysis. Genes in an organism’s DNA (genome) have embedded ... typical bacterial genome contains on the order of 5,000 genes. Mammalian genomes can contain ... tens of thousands of genes. For each genome sequenced, the challenge is to identify protein ... organisms. But, the memory footprint of sequence data is growing more rapidly than per-node...
  • NAST

  • Referenced in 3 articles [sw13835]
  • rRNA genes. Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments ... such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool ... characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed ... researchers with various experience levels to obtain bacterial and archaeal community profiles...
  • ASA3P

  • Referenced in 1 article [sw38149]
  • higher-level analyses pipeline for closely related bacterial isolates. ASA³P is a fully automatic ... scalable assembly, annotation and higher-level analysis pipeline creating results in standard bioinformatics file formats ... data of multiple closely related isolates, thus transforming raw reads into assembled and annotated genomes ... gathering as much information on every single bacterial genome as possible. Per-isolate analyses...
  • Prokka

  • Referenced in 2 articles [sw16996]
  • these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce ... tool to fully annotate a draft bacterial genome in about ten minutes on a typical ... produces standards-compliant output files for further analysis or viewing in genome browsers. Availability...
  • RNAmmer

  • Referenced in 1 article [sw16998]
  • genes. The publication of a complete genome sequence is usually accompanied by annotations ... program uses hidden Markov models trained on data from the 5S ribosomal RNA database ... sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results...
  • QuartetS

  • Referenced in 2 articles [sw34206]
  • unparalleled growth in the availability of genomic data offers both a challenge to develop orthology ... leveraging evolutionary evidence in the accumulated sequenced genomes. Here, we report a novel orthology detection ... homologous genes, QuartetS uses an approximate phylogenetic analysis of quartet gene trees to infer ... QuartetS followed by clustering)], involving 624 bacterial genomes and >2 million genes. We found that...
  • SneakerNet

  • Referenced in 1 article [sw38144]
  • published workflows for performing an analysis on primary sequence data that span the breadth ... pipeline can be given a set of genomes to run analyses: species inference, 7-gene ... plugins based architecture for batches of unrelated bacterial sequences or for batches of bacteria from...
  • GAP

  • Referenced in 3164 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • Matlab

  • Referenced in 13488 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9832 articles [sw00771]
  • R is a language and environment for statistical...
  • Graphviz

  • Referenced in 90 articles [sw01283]
  • Graphviz is open source graph visualization software. Graph...
  • MIRA

  • Referenced in 1 article [sw02392]
  • MIRA is a multi-pass DNA sequence data...
  • STAR

  • Referenced in 15 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • Bioconductor

  • Referenced in 320 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • fda (R)

  • Referenced in 1531 articles [sw04511]
  • fda: Functional Data Analysis , These functions were developed...
  • Rfam

  • Referenced in 33 articles [sw04637]
  • The Rfam database is a collection of RNA...
  • Rnamotif

  • Referenced in 10 articles [sw04638]
  • The rnamotif program [1] searches a database for...
  • LIBSVM

  • Referenced in 1185 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • GlobPlot

  • Referenced in 7 articles [sw06213]
  • GlobPlot: exploring protein sequences for globularity and disorder...
  • SAS

  • Referenced in 1552 articles [sw06377]
  • SAS (Statistical Analysis System) is an integrated system...