• POSSUM

  • Referenced in 8 articles [sw24532]
  • bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. Evolutionary information ... highly informative representation of protein sequences. Accordingly, PSSM-based feature descriptors have been successfully applied...
  • PseDNA-Pro

  • Referenced in 6 articles [sw22424]
  • vector composed of three kinds of sequence-based features, including overall amino acid composition, pseudo ... physicochemical distance transformation. These features not only consider the sequence composition of proteins, but also...
  • NR-2L

  • Referenced in 9 articles [sw26879]
  • identifying nuclear receptor subfamilies based on sequence-derived features. Nuclear receptors ... nuclear receptor or not based on its sequence information alone; if it is, the prediction ... based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features ... derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor...
  • WoLF PSORT

  • Referenced in 11 articles [sw27721]
  • converts protein amino acid sequences into numerical localization features; based on sorting signals, amino acid ... features to the query, and (ii) tables with detailed information about individual localization features ... convenience, sequence alignments of the query to similar proteins and links to UniProt and Gene...
  • MemHyb

  • Referenced in 15 articles [sw25194]
  • membrane protein types based on their primary sequence. In this paper, we tackle the interesting ... types using their sequence information. We consider both evolutionary and physicochemical features and provide them ... classification system based on support vector machine (SVM) with error correction code. We employ ... powerful sequence encoding scheme by fusing position specific scoring matrix and split amino acid composition...
  • iEzy-drug

  • Referenced in 15 articles [sw22455]
  • drugs in cellular networking. With the features of extremely high selectivity and efficiency in catalyzing ... computational methods were developed in this regard based on the knowledge of the three-dimensional ... still unknown. Here, we reported a sequence-based predictor, called ”iEzy-Drug,” in which each ... sequential evolution information and physicochemical features derived from its sequence, and the prediction engine...
  • iFeature

  • Referenced in 5 articles [sw27776]
  • peptide sequences. iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation...
  • propy

  • Referenced in 27 articles [sw22402]
  • Geary autocorrelation, sequence-order-coupling number, quasi-sequence-order descriptors, composition, transition and distribution ... pseudo amino acid composition (PseAAC) descriptors. These features could be generally regarded as different Chou ... also easily compute the previous descriptors based on user-defined properties, which are automatically available...
  • CAP3

  • Referenced in 16 articles [sw08935]
  • sequence assembly program. The CAP3 program includes a number of improvements and new features ... uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments...
  • CONLIN

  • Referenced in 46 articles [sw14151]
  • based on convex approximation concepts. The Convex Linearization method (CONLIN) exhibits many interesting features ... optimization problem is therefore replaced with a sequence of explicit approximate problems having a simple...
  • ESLpred

  • Referenced in 20 articles [sw22403]
  • location of eukaryotic proteins from their different features such as amino acid composition, dipeptide composition ... module based on dipeptide composition performed better than the SVM modules based on amino acid ... also used to search the query sequence against the dataset of proteins (experimentally annotated proteins ... developed a hybrid module using all features of a protein, which consisted of an input...
  • EpiLoc

  • Referenced in 3 articles [sw22452]
  • EpiLoc: a (working) text-based system for predicting protein subcellular location. MOTIVATION: Predicting the subcellular ... integration of text features into a sequence-based classifier to improve location prediction performance. RESULTS ... text-based component itself. We introduce EpiLoc, a comprehensive text-based localization system. We provide ... depth study of text-feature selection, and study several new ways to associate text with...
  • iNuc-PhysChem

  • Referenced in 24 articles [sw22453]
  • iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties. Nucleosome positioning ... twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome...
  • repDNA

  • Referenced in 12 articles [sw16473]
  • sequence-order information via the physicochemical properties of its constituent oligonucleotides. In addition, these features ... easily calculated based on both the built-in and user-defined properties via using repDNA...
  • BEDTools

  • Referenced in 11 articles [sw17302]
  • However, searching for overlaps between features with existing web-based methods is complicated ... datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore ... comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature...
  • CONTRAlign

  • Referenced in 4 articles [sw08305]
  • signals in sequence alignment: using CONTRAlign, we find that hydropathy-based features result in improvements...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • that share twilight-zone pairwise similarity with sequences used for the prediction. Results: SCPRED uses ... custom-designed features as its input to predict the structural classes. Based on extensive design ... with PSI-PRED and one feature computed from the sequence. Tests performed with datasets ... find similar structures for sequences that share low identity with sequence used for the prediction...
  • DENFIS

  • Referenced in 58 articles [sw24183]
  • accommodate new input data, including new features, new classes, etc., through local element tuning ... calculated through a fuzzy inference system based on m-most activated fuzzy rules which ... that DENFIS can effectively learn complex temporal sequences in an adaptive way and outperform some...
  • Minfi

  • Referenced in 6 articles [sw23478]
  • range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product...
  • PROFEAT

  • Referenced in 14 articles [sw16924]
  • descriptors and 1447 descriptor values. The computed features include amino acid composition, dipeptide composition, normalized ... Moran autocorrelation, Geary autocorrelation, sequence-order-coupling number, quasi-sequence-order descriptors and the composition ... also compute previous autocorrelations descriptors based on user-defined properties. Our computational algorithms were extensively ... tested and the computed protein features have been used in a number of published works...