• PSI-BLAST

  • Referenced in 235 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...
  • Cd-hit

  • Referenced in 49 articles [sw16887]
  • than methods based on the popular sequence comparison and database search tools, such as BLAST...
  • FASTA

  • Referenced in 25 articles [sw09655]
  • Rapid and sensitive sequence comparison with FASTP and FASTA. The FASTA program can search ... high scores were fortuitous. As sequence comparison methods become more powerful by becoming more sensitive...
  • MODELLER

  • Referenced in 34 articles [sw27731]
  • sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER...
  • Mauve

  • Referenced in 16 articles [sw24606]
  • processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes ... frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments ... quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome...
  • ProbCons

  • Referenced in 16 articles [sw12014]
  • novel scoring function for multiple sequence comparisons. We present ProbCons, a practical tool for progressive...
  • MEGAN

  • Referenced in 17 articles [sw33189]
  • common habitat using targeted or random sequencing. Goals include understanding the extent and role ... sample is usually estimated by comparison against sequence databases of known sequences. Most published studies ... against databases of known sequences using BLAST or another comparison tool. MEGAN is then used ... reflects the level of conservation of the sequence. The software allows large data sets...
  • COMPASS

  • Referenced in 9 articles [sw23109]
  • present a novel method for the comparison of multiple protein alignments with assessment of statistical ... BLAST approach to profile-sequence comparison, which is adapted for the profile-profile case. Tested ... methods for profile-sequence (PSI-BLAST) and profile-profile (prof_sim) comparison, COMPASS shows increased...
  • ELM

  • Referenced in 8 articles [sw17021]
  • fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate...
  • FASTA3

  • Referenced in 7 articles [sw15724]
  • years ago (1), DNA and protein sequence comparisons have become routine steps in biochemical characterization ... entire genomes. As the DNA and protein sequence databases become more complete, a sequence similarity...
  • RepeatMasker

  • Referenced in 7 articles [sw17266]
  • identified and masked by the program. Sequence comparisons in RepeatMasker are performed ... Dfam ( profile HMM library derived from Repbase sequences ) and Repbase, a service of the Genetic...
  • BEDTools

  • Referenced in 11 articles [sw17302]
  • datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore ... introduces a new software suite for the comparison, manipulation and annotation of genomic features ... format. BEDTools also supports the comparison of sequence alignments in BAM format to both...
  • Cluster-C

  • Referenced in 6 articles [sw10932]
  • proved that all-vs-all massive sequence comparisons may be an effective approach ... Cluster-C allows a large number of sequences to be classified in such...
  • LASSAP

  • Referenced in 3 articles [sw33234]
  • LASSAP, a large scale sequence comparison package. This paper presents LASSAP, a new software package ... sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations ... sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides ... hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string...
  • MARNA

  • Referenced in 5 articles [sw35539]
  • structure prediction of RNAs based on sequence structure comparisons. Results: We describe a novel approach ... structures. It is based on pairwise sequence–structure comparisons of RNAs. From these sequence–structure...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three ... global-local algorithm to align a sequence-structure pair when they greatly differ in length...
  • Symstra

  • Referenced in 19 articles [sw01296]
  • generation tasks using symbolic execution of method sequences with symbolic arguments. The paper defines symbolic ... states of object-oriented programs and novel comparisons of states. Given a set of methods ... bound on the length of sequences, Symstra systematically explores the object-state space ... prunes this exploration based on the state comparisons. Experimental results show that Symstra generates unit...
  • PCMA

  • Referenced in 4 articles [sw24612]
  • combines two different alignment strategies. Highly similar sequences are aligned in a fast ... relatively divergent groups based on profile-profile comparison and consistency. The scoring function for local ... BLAST approach to profile-sequence comparison. PCMA balances speed and accuracy in a flexible ... suitable for aligning large numbers of sequences. AVAILABILITY: PCMA is freely available for non-commercial...
  • BEETL

  • Referenced in 5 articles [sw23284]
  • Comparing DNA sequence collections by direct comparison of compressed text indexes. Popular sequence alignment tools ... that an all-against-all comparison of two sequence collections can be computed from...
  • rVISTA

  • Referenced in 4 articles [sw18501]
  • rVISTA tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions ... present in a specific configuration within genomic sequences. Here, we present the newly developed version...