• UniProt

  • Referenced in 128 articles [sw21320]
  • majority of sequences coming from genome sequencing projects. We have created a new proteome identifier...
  • iRSpot-PseDNC

  • Referenced in 65 articles [sw22437]
  • time-consuming. With the avalanche of genome sequences generated in the postgenomic ... predictor, the samples of DNA sequences are formulated by a novel feature vector ... extended to deal with all the other genomes. Particularly, it has not escaped our notice...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • information, particularly the global or long-range sequence order information, via the physicochemical properties ... many problems in computational genomics and genome sequence analysis. However, dealing with different ... useful tool in computational genomics and genome sequence analysis...
  • JASPAR

  • Referenced in 39 articles [sw18502]
  • analysis of regulatory regions in genome sequences is strongly based on the detection of potential ... online sequence analysis utility and a suite of programming tools for genome‐wide and comparative...
  • BioProspector

  • Referenced in 27 articles [sw09375]
  • genes. The development of high throughput genome sequencing and gene expression techniques gives rise ... computed from the whole genome sequences. A new motif scoring function is adopted to allow ... each input sequences to contain zero to multiple copies of the motif. In addition, BioProspector ... find s54 motif from M. xanthus genome, many B. subtilis motifs from DBTBS collection...
  • iNuc-PseKNC

  • Referenced in 31 articles [sw16607]
  • iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo ... cellular processes. With the avalanche of genome sequences generated in the post-genomic ... determining the nucleosome positioning on a DNA sequence. Results: Here a predictor called ‘iNuc-PseKNC ... Drosophila melanogaster genomes, respectively. In the new predictor, the samples of DNA sequences were formulated...
  • iRSpot-TNCPseAAC

  • Referenced in 31 articles [sw22412]
  • With the ever-increasing amount of genome sequence data in the postgenomic era, computational methods ... meiotic recombination and the process of genome evolution as well. To meet the need ... incorporate its local or short-rage sequence order information; while the latter, its global ... sequence order information into a discrete model may also be used for many other genome...
  • iPro54-PseKNC

  • Referenced in 32 articles [sw22411]
  • iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo ... promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen ... related genes. With the avalanche of genome sequences generated in the postgenomic...
  • iRSpot-EL

  • Referenced in 29 articles [sw24776]
  • growth. With the avalanche of genome sequences emerging in the post-genomic...
  • E-CELL

  • Referenced in 20 articles [sw07917]
  • environment for whole-cell simulation. MOTIVATION: Genome sequencing projects and further systematic functional analyses ... known chromosome, whose complete 580 kb genome sequence was determined at TIGR ... CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available...
  • MetaCyc

  • Referenced in 27 articles [sw08243]
  • metabolic pathways of organisms from their sequenced genomes, supporting metabolic engineering, helping to compare biochemical...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • avalanche of biological sequences generated in the post-genomic age, one of the most challenging ... biology is how to effectively formulate the sequence of a biological sample (such ... feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those feature ... tool in computational proteomics, genomics, as well as biological sequence analysis. Moreover, to maximize users...
  • Velvet

  • Referenced in 23 articles [sw17026]
  • manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact...
  • MUMMER

  • Referenced in 39 articles [sw17256]
  • protein sequences. MUMmer is a system for rapidly aligning entire genomes, whether in complete ... sequencing project, and will align them to another set of contigs or a genome using ... species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer ... frame translations of both input sequences. The original MUMmer system, version 1.0, is described...
  • BLASTZ

  • Referenced in 11 articles [sw22996]
  • Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment ... various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed ... specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain...
  • RSEM

  • Referenced in 11 articles [sw17160]
  • data with or without a reference genome. Background: RNA-Seq is revolutionizing the way transcript ... transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which ... software does not require a reference genome. Thus, in combination with a de novo transcriptome ... accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM...
  • iTIS-PseTNC

  • Referenced in 15 articles [sw22449]
  • iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using ... genome analysis. With the avalanche of genome sequences generated in the postgenomic...
  • Mauve

  • Referenced in 11 articles [sw24606]
  • Mauve: multiple alignment of conserved genomic sequence with rearrangements. As genomes evolve, they undergo large ... comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces ... sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome...
  • tRNAscan-SE

  • Referenced in 15 articles [sw08005]
  • detection of transfer RNA genes in genomic sequence. We describe a program, tRNAscan-SE, which...
  • iSS-PseDNC

  • Referenced in 15 articles [sw22438]
  • gene expression. With the avalanche of genome sequences generated in the postgenomic...