• Minimap2

  • Referenced in 1 article [sw28780]
  • Minimap2: pairwise alignment for nucleotide sequences. Recent advances in sequencing technologies promise ultra-long reads...
  • SSW Library

  • Referenced in 1 article [sw33167]
  • algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used...
  • C-GRAAL

  • Referenced in 3 articles [sw08317]
  • sequence comparison and alignment. Here, we introduce a novel pairwise global alignment algorithm called Common...
  • ppALIGN

  • Referenced in 1 article [sw10264]
  • reliability of score-based pairwise alignments of DNA or protein sequences. The design ... analyze the outcomes of popular score based aligners and search tools without having to choose ... standalone program for user defined alignments (ppALIGN) and another program (ppBLAST) which can process ... detect and quantify questionable regions in pairwise alignments. Due to its structure, the input/output interface...
  • BIONJ

  • Referenced in 29 articles [sw08301]
  • when these estimates are obtained from aligned sequences. At each step it permits the selection ... When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site...
  • tracker2

  • Referenced in 1 article [sw15710]
  • alternative local multiple sequence alignments from a collection of local pairwise alignments arises naturally ... used to identify regulatory elements by comparative sequence analysis. Based on a theoretical discussion...
  • G-MAPSEQ

  • Referenced in 1 article [sw22762]
  • fragment of reference sequence) and exact, ultrafast semiglobal pairwise alignment method which is performed...
  • SARSA

  • Referenced in 4 articles [sw13834]
  • sequences and determine their structural similarities. In SARSA, we provide two RNA structural alignment tools ... PARTS for pairwise alignment of RNA tertiary structures and MARTS for multiple alignment...
  • PMFastR

  • Referenced in 1 article [sw24608]
  • pairwise RNA structure alignments and then build the multiple alignment using only the sequence information...
  • DIAL

  • Referenced in 6 articles [sw13837]
  • pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that ... dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity and (iii) nucleotide base-pairing similarity...
  • Darwin

  • Referenced in 1 article [sw35912]
  • computational biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment...
  • rVISTA

  • Referenced in 3 articles [sw18501]
  • present in a specific configuration within genomic sequences. Here, we present the newly developed version ... alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise ... collection or search for user-defined consensus sequences. The rVISTA tool is publicly available...
  • Decombinator

  • Referenced in 1 article [sw23150]
  • published human TcR-β sequences. Decombinator assigned sequences at a rate more than two orders ... faster than that achieved by classical pairwise alignment algorithms, and with a high degree ... error rates in the in silico sequences. Analysis of the published sequence dataset highlighted...
  • libgapmis

  • Referenced in 2 articles [sw24065]
  • alignment between a substring of the reference sequence succeeding and the remaining suffix ... libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version ... traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions ... alignment. CONCLUSIONS: We present libgapmis, a library for extending pairwise short-read alignments. We show...
  • DAFS

  • Referenced in 1 article [sw17125]
  • sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment ... DAFS decomposes the pairwise structural alignment problem into two independent secondary structure prediction problems ... pairwise structural alignment by imposing penalties on inconsistent base pairs and alignment columns that ... DAFS can produce reliable structural alignments from unaligned sequences in terms of accuracy of common...
  • STELLAR

  • Referenced in 1 article [sw34362]
  • genomic sequences requires reliable tools for the search of local alignments. Practical local aligners ... matches. We provide here the local pairwise aligner STELLAR that has full sensitivity, i.e. guarantees ... minimal length and maximal error rate. The aligner is composed of two steps, filtering ... very practical and fast on very long sequences which makes it a suitable new tool...
  • iPARTS

  • Referenced in 4 articles [sw13839]
  • pairwise alignment of RNA tertiary structures. PARTS is an improved web server for aligning ... transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical...
  • EFICAz

  • Referenced in 3 articles [sw35281]
  • classification (CHIEFc), (ii) pairwise sequence comparison using a family specific Sequence Identity Threshold, (iii) recognition ... information from homofunctional and heterofunctional multiple sequence alignments associated with an enzyme family. The FDRs...
  • FsePSA

  • Referenced in 0 articles [sw17418]
  • aligning CDS, either by amino acid sequence alignment back-translation, or by simultaneously accounting ... scheme with an algorithm for the pairwise alignment of CDS accounting for frameshift translation initiation ... simultaneously accounting for nucleotide and amino acid sequences. We compare the method to other...
  • TCS

  • Referenced in 1 article [sw24605]
  • modeling procedure when analyzing biological sequences. Homology and evolutionary modeling are the most common applications ... from BAliBASE and PREFAB structure-based reference alignments. We also show how this measure ... Coffee framework; it uses libraries of pairwise alignments to evaluate any third party MSA. Pairwise...