• BLAST

  • Referenced in 241 articles [sw17334]
  • sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical...
  • PSI-BLAST

  • Referenced in 226 articles [sw17324]
  • protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic ... more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover...
  • UniProt

  • Referenced in 128 articles [sw21320]
  • UniProt is an important collection of protein sequences and their annotations, which has doubled ... help users track the provenance of sequences. We present a new website that has been ... relative amount of knowledge known about each protein. These scores will be helpful in identifying...
  • MUSCLE

  • Referenced in 71 articles [sw13193]
  • Muscle: multiple sequence alignment with high accuracy and high throughput. We describe MUSCLE ... program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance...
  • Cd-hit

  • Referenced in 46 articles [sw16887]
  • comparing large sets of protein or nucleotide sequences. Motivation: In 2001 and 2002, we published ... describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster ... huge protein database with millions of sequences. However, the applications of the underlying ... algorithm are not limited to only protein sequences clustering, here we present several new programs...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • pseudo components of DNA, RNA, and protein sequences. With the avalanche of biological sequences generated ... formulate the sequence of a biological sample (such as DNA, RNA or protein) with ... difficult for users to formulate the biological sequences according to their desired features or properties ... feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those feature...
  • GPCR-CA

  • Referenced in 35 articles [sw25949]
  • receptor functional classes. Given an uncharacterized protein sequence, how can we identify whether ... piles of long and complicated protein sequences. Meanwhile, the gray-level co-occurrence matrix factors ... which none of proteins has >or=40% pairwise sequence identity to any other ... layer results for a query protein sequence within about 20 seconds...
  • Memtype-2L

  • Referenced in 39 articles [sw16472]
  • through pse-PSSM. Given an uncharacterized protein sequence, how can we identify whether ... system. Particularly, with the avalanche of protein sequences generated in the Post-Genomic ... prediction engine is to identify a query protein as membrane or non-membrane...
  • PISCES

  • Referenced in 31 articles [sw16873]
  • PISCES: a protein sequence culling server. Summary: PISCES is a public server for culling sets ... protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria ... chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with ... matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than...
  • DIALIGN

  • Referenced in 33 articles [sw12015]
  • DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. DIALIGN is a widely used software ... tool for multiple DNA and protein sequence alignment. The program combines local and global alignment...
  • iSNO-PseAAC

  • Referenced in 39 articles [sw22446]
  • universal PTMs. With the avalanche of protein sequences generated in the post-genomic ... timely identifying the exact SNO sites in proteins because this kind of information is very ... derived from the proteins that had [Formula: see text] pairwise sequence identity to any other ... achieved by iSNO-PseAAC in identifying nitrosylated proteins on an independent dataset was over...
  • Signal-CF

  • Referenced in 30 articles [sw26854]
  • cleavage sites in eukaryotic and bacterial protein sequences. It is a 2-layer predictor ... prediction engine is to identify a query protein as secretory or non-secretory ... subsite coupling effects along a protein sequence and by fusing the results derived from many...
  • Cell-PLoc

  • Referenced in 90 articles [sw09126]
  • than or equal to25% sequence identity to any other protein in the same subcellular-location...
  • 2D-MH

  • Referenced in 21 articles [sw19727]
  • server for generating graphic representation of protein sequences based on the physicochemical properties of their ... proposed to represent protein sequences. It is formed by incorporating the information of the side ... reflecting the innate structure of the protein sequence, (3) clear visibility in displaying the similarity ... protein sequences, (4) more sensitive for the mutation sites important for drug targeting...
  • PAML

  • Referenced in 40 articles [sw10916]
  • phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed...
  • MUMMER

  • Referenced in 39 articles [sw17256]
  • alignment of large-scale DNA and protein sequences. MUMmer is a system for rapidly aligning...
  • MODELLER

  • Referenced in 33 articles [sw27731]
  • protein three-dimensional structures (1,2). The user provides an alignment of a sequence ... hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints ... defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases...
  • FASTA

  • Referenced in 25 articles [sw09655]
  • FASTA program can search the NBRF protein sequence library (2.5 million residues) in less than ... microcomputer and unambiguously detect proteins that shared a common ancestor billions of years ... finding distantly related members of the G-protein-coupled receptor family. The joining step ... FASTA were designed to identify protein sequences that have descended from a common ancestor...
  • iSuc-PseOpt

  • Referenced in 23 articles [sw22429]
  • Identifying lysine succinylation sites in proteins by incorporating sequence-coupling effects into pseudo components ... residue of a protein molecule. Lysine succinylation plays an important role in orchestrating various biological ... drug development: given an uncharacterized protein sequence containing many Lys residues, which one of them ... cannot? With the avalanche of protein sequences generated in the postgenomic age, the answer...
  • AFP-Pred

  • Referenced in 24 articles [sw22441]
  • random forest approach for predicting antifreeze proteins from sequence-derived properties. Some creatures living ... produce some special materials called ”antifreeze proteins” (AFPs), which can prevent the cell and body ... prediction of antifreeze proteins from protein sequence. AFP-Pred was trained on the dataset containing ... useful approach to identify antifreeze proteins from sequence information, irrespective of their sequence similarity...