*  Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase | SpringerLink
... multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26:320-322CrossRefGoogle Scholar ... flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882CrossRef ... a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540 ... Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R (1998) Pfam: ...
  https://link.springer.com/article/10.1007%2Fs12154-010-0040-8
*  MAFFT: Iterative Refinement and Additional Methods | SpringerLink
MAFFT is a popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative... ... Gotoh O (1993) Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl ... combining protein sequences and structures within multiple sequence alignments. J Mol Biol 340:385-395PubMedCrossRefGoogle ... Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol 5:21PubMedCrossRef ...
  https://link.springer.com/protocol/10.1007%2F978-1-62703-646-7_8
*  CMU-ISRI-04-134.ps | Single Nucleotide Polymorphism | Sequence Alignment
The number of gaps generalized for each sequence in all sets, is 0.5 or less, which suggests that multiple sequence alignments ... For each sequence, which we call the referring sequence, the set of closest sequences, or proposed sequences, as designated by ... where the sequences were used for analysis of general sequence variation. The second set of sequences consists of 30 sequences ... proposed below anonymizes DNA sequences by generalizing each sequence and its most similar sequence to a common sequence. Thus ...
  https://www.scribd.com/document/2521719/CMU-ISRI-04-134-ps
*  Sequence alignment package for LaTeX?
Does anyone happen to know of a package for displaying sequence , alignments in LaTex? I use alscript and then import ... Sequence alignment package for LaTeX?. Francois Jeanmougin pingouin at crystal.u-strasbg.fr Wed Aug 12 06:42:06 EST 1998 * ...
  http://www.bio.net/bionet/mm/bio-soft/1998-August/019270.html
*  Frontiers | A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major...
Of these CSIs, a 3 aa insert in the FlgC protein is uniquely shared by all sequenced Spirochaetes providing a molecular marker ... Of these CSIs, a 3 aa insert in the FlgC protein is uniquely shared by all sequenced Spirochaetes providing a molecular marker ... Treponema distinct from the genus Borrelia is also strongly supported by phylogenetic trees based upon concatenated sequences ... Treponema distinct from the genus Borrelia is also strongly supported by phylogenetic trees based upon concatenated sequences ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2013.00217/full
*  Multiple Sequence Alignment by Ant Colony Optimization and Divide-and-Conquer | SpringerLink
Obtaining an accurate alignment of protein sequences is a difficult computational problem because many heuristic... ... Multiple sequence alignment is a common task in molecular biology and bioinformatics. ... Gotoh, O.: Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinements as Assessed by ... Multiple Sequence Alignment High Quality Solution Frequency Assignment Problem Sequence Alignment Method Future Generation ...
  https://link.springer.com/chapter/10.1007/11758525_88
*  Identification and characterization of a salivary adenosine deaminase from the sand fly Phlebotomus duboscqi, the vector of...
Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23,403 -405. ... Clustal alignments of invertebrate putative salivary adenosine deaminase (ADA) of P. duboscqi (PduM73 and PduM74), Lutzomyia ... Consensus protein sequences were compared to related sequences from sand flies as well as non-sand fly species obtained from ... integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5, 150-163. ...
  http://jeb.biologists.org/content/210/5/733
*  Sequence Alignments on the WWW or FTP
... for ,'multiple sequence alignment'. However, I did not find ,the same format at each site, and most sites provided ,text ... Sequence Alignments on the WWW or FTP. Dr. Andrew G. McArthur mcarthur at onyx.si.edu Tue May 12 16:24:50 EST 1998 *Previous ... I just went searching for pre-built multiple sequence ,alignments on which to test some phylogenetic software. , , I found ... At the HIV Database, we try to provide both text ,and more machine-readable formats for our alignments. ,Is FASTA format the ' ...
  http://www.bio.net/hypermail/molecular-evolution/1998-May/006337.html
*  Sequence alignment - Wikipedia
Computational approaches to sequence alignment generally fall into two categories: global alignments and local alignments. ... Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple ... Sequence homology Sequence mining BLAST String searching algorithm Alignment-free sequence analysis UGENE Needleman-Wunsch ... like the problem of selecting the optimal multiple sequence alignment, is NP-hard. Sequence alignments are useful in ...
  https://en.wikipedia.org/wiki/Sequence_alignment
*  Refining multiple sequence alignments with conserved core regions
It seems that improvement of the alignment score largely depends on the sequence diversity of the input alignments. Our results ... Here the PSSM is indexed by alignment column i and the corresponding residues, AA from the sequence 'r'. The 'alignment score ... The alignment refinement algorithm has been applied to 362 CDD multiple alignments and 900 PFAM (1) alignments derived by both ... One way to validate the multiple alignment method is to examine its performance of produced alignment or sequence profile in ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC1463900/?lang=en-ca
*  Multiple sequence alignment - Wikipedia
Multiple sequence alignment viewers enable alignments to be visually reviewed, often by inspecting the quality of alignment for ... tree alignment Phylogenetics Sequence alignment software Multiple sequence alignment viewers Structural alignment Alignment- ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ... Multiple sequence alignment also refers to the process of aligning such a sequence set. Because three or more sequences of ...
  https://en.wikipedia.org/wiki/Multiple_sequence_alignment
*  Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes | BMC Bioinformatics | Full Text
12859_2004_331_MOESM4_ESM.rtf Additional File 4: Relevant Sequence Alignments Protein sequence alignments upon which ... Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000 ... 12859_2004_331_MOESM3_ESM.txt Additional File 3: Protein sequences of all sequences analysed in this manuscript. Sequences are ... 37] [see additional files 1, 2, 3]. Sequence alignments were performed using the ClustalX [65] or T-COFFEE algorithms [66]and ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-6
*  A model of evolution and structure for multiple sequence alignment | Philosophical Transactions of the Royal Society B:...
Using alignment anchoring, the pairwise alignments of human and mouse sequences took approximately 600 and 1500 s on an AMD ... sequences in an alignment can be seen as descendants of an ancestral sequence or a set of sequences sharing a common or a ... We consider a pairwise alignment of sequences x and y consisting of characters x1 … xn and y1 … ym. Sequence sites are ... As expected, the alignment of very close sequences, such as human and chimpanzee, does not provide information on the sequence ...
  http://rstb.royalsocietypublishing.org/content/363/1512/3913
*  Pfam - Wikipedia
... a representative subset of sequences are aligned into a high-quality seed alignment. Sequences for the seed alignment are taken ... Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden ... manually checked seed alignment, as well as a full alignment built by aligning sequences to a profile hidden Markov model built ... This seed alignment is then used to build a profile hidden Markov model using HMMER. This HMM is then searched against sequence ...
  https://en.wikipedia.org/wiki/Pfam
*  The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin | Springer for Research & Development
... sequence alignment and phylogeny approach. Alignments of representative sequences from the 24kD/51kD domains were generated ... A multiple sequence alignment of the "mitochondrial" complex I subunits and 24 kDa/hoxF and 51 kDa/hoxU -like sequences of the ... Galtier N, Gouy M, Gautier C: SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput ... Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ: Multiple sequence alignment with Clustal X. Trends Biochem Sci. 1998 ...
  https://rd.springer.com/article/10.1186/1471-2148-7-230
*  List of sequence alignment software - Wikipedia
"Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU". Parallel and Distributed ... This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment ... Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: ... Alignment type: local or global *Sequence type: protein or nucleotide *Sequence type: protein or nucleotide Please see List of ...
  https://en.wikipedia.org/wiki/List_of_sequence_alignment_software
*  Differential Expression of Glutamate Receptor Subunits in the Nervous System of Caenorhabditis elegans and Their Regulation by...
Partial sequence alignments of predicted C. elegans ionotropic glutamate receptors. Sequence alignment of a highly conserved ... 1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position- ... Sequence alignment of C. elegans,Drosophila, and rat ionotropic glutamate receptor subunits beginning immediately at TMI and ... 7, Table 2). Both GLR-7 and GLR-8 are outliers in the sequence alignment, and GLR-8 cannot be obviously categorized into NMDA ...
  http://www.jneurosci.org/content/21/5/1510.long
*  DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment | BMC Bioinformatics | Full Text
... but there is wide difference between global and local alignments. For a global alignment A g that covers most of the sequences ... Objective functions for sequence alignment. From a computer scientist's point-of-view, sequence alignment is an optimisation ... of the total sequence length are homologous to other sequences in the respective sequence families. Also, the sequences in ... For protein alignment, one of the usual substitution matrices can be used; for alignment of DNA or RNA sequences, the program ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-66
*  Optimization of sequence alignment for simple sequence repeat regions | BMC Research Notes | Full Text
A comparison between two alignments of the sequence of case A by using MEGA4 software (A) and the new software prepared in this ... Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering ... of the whole sequence. After applying the alignment in the MEGA 4 alignment and our modifications, one major difference was ... Sequence alignment involves the identification of the correct location of INDELS that have happened since their divergence from ...
  https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-4-239
*  DWNN, a novel ubiquitin-like domain, implicates RBBP6 in mRNA processing and ubiquitin-like pathways | BMC Structural Biology |...
... and sequence alignments were generated using ClustalX [39]. Details of the sequences used in Figure 2 can be found in ... An alignment of DWNN homologues from a range of different eukaryotes is shown in Figure 2. These sequences show no similarity ... Sequence alignment of DWNN homologues from a range of eukaryotic genomes. The DWNN domain has been found in all eukaryotic ... D) Structural alignment of the primary sequences of DWNN and ubiquitin, determined using the Dali server. The structurally ...
  https://bmcstructbiol.biomedcentral.com/articles/10.1186/1472-6807-6-1
*  Algorithms currently supported by the Sockeye Platform (through Chinook) - Canada's Michael Smith Genome Sciences Centre
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific ... Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563- ... T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217. Annotations. Eponine ... DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics 14, 1998, 290-294. Lagan and MultiLagan ...
  http://www.bcgsc.ca/project/bomge/sockeye/algorithms
*  X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific ... Each family in Pfam is represented by two multiple sequence alignments and two profile-Hidden Markov Models (profile-HMMs) [1 ... search of Uniprot protein sequence database using the sequences of both 10093b and 10093f yielded 61 matches (sequence ... Multiple sequence alignment of DUF178 from various organisms. The residues highlighted in orange are the conserved residues ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2174479/?lang=en-ca
*  Genomic organization and evolution of the ULBP genes in cattle | BMC Genomics | Full Text
Internal sequence identity plot of the minor ULBP cluster. Sequence numbers displayed on the X- and Y-axes indicate alignment ... Comparison of nucleotide alignments in the cattle minor ULBP cluster and HSA12 genomic sequence demonstrates that sequence ... Internal sequence identity plot of the major ULBP cluster. Sequence numbers displayed on the X- and Y-axes indicate alignment ... For the two BACs sequenced in the second round, sequence gaps were closed by primer walking. Contiguous sequences [GenBank: ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-227
*  Microbiology Society Journals | Isolation and full-length sequence analysis of Armigeres subalbatus totivirus, the first...
Full genome sequence analysis showed the virus to be related to members of the family Totiviridae, and was therefore named ' ... improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap ... multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26, 320-322.. ... Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.[CrossRef] ...
  http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/vir.0.024794-0
*  Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum |...
No effective treatment is available and the genome sequence has recently been completed. This parasite differs from other ... Region of leucine aminopeptidase multiple sequence alignment that illustrates several characters uniting apicomplexan sequences ... New multiple sequence alignments were created with ClustalX [66], followed by manual refinement. Only unambiguously aligned ... The remaining sequence was represented by two independently isolated expressed sequence tag (EST) sequences in the GenBank and ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-11-r88