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
... is a powerful integrative toolthat addresses a variety of biological problems, ranging from key functional ... Gotoh O (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed ... Durbin R, Eddy S, Krogh A and Mitchison G (1999) Multiple sequence alignment methods. In: Durbin R (ed.) Biological Sequence ... Finally, the myosin‐binding protein sequence is aligned with the twitchin sequence, before being merged with the alignment of ...http://www.els.net/WileyCDA/ElsArticle/refId-a0005258.html
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 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
Replacing dietary fish oil by vegetable oils has little effect on lipogenesis, lipid transport and tissue lipid uptake in...
Higgins, DG, Sharp, PM, Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci (1998) 5 151-153 ... Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ, Basic local alignment search tool. J Mol Biol (1990) 215 403-410. ... Biochim Biophys Acta (1998) 967 354-363.. Bell, JG, McEvoy, J, Tocher, DR, McGhee, F, Campbell, PJ, Sargent, JR, Replacement of ... J Nutr (1998) 128 444S-448S.. Fernandez, ML, West, KL, Mechanisms by which dietary fatty acids modulate plasma lipids. J Nutr ( ...https://www.cambridge.org/core/journals/british-journal-of-nutrition/article/replacing-dietary-fish-oil-by-vegetable-oils-has-little-effect-on-lipogenesis-lipid-transport-and-tissue-lipid-uptake-in-rainbow-trout-oncorhynchus-mykiss/AD57E9001B8D4E4AA4E08B89BE6B3F7F
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
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
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  or T-COFFEE algorithms and ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-6
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
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
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega | Molecular Systems Biology
Clustal Omega also can align sequences to existing alignments using conventional alignment methods. Users can add sequences to ... Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the ... based alignment of at least five sequences. These sequences are then inserted into a test set of sequences from the ... Results from testing large alignments with up to 50 000 sequences are given in Table III using HomFam. Here, each alignment is ...http://msb.embopress.org/content/7/1/539
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
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
Reticular alignment: A progressive corner-cutting method for multiple sequence alignment | BMC Bioinformatics | Full Text
... it defines a set of optimal and suboptimal alignments at each step during the progressive alignment. The set of alignments are ... the deeper the search in the alignment space for better scored alignments. We implemented the program in the Java programming ... Reticular alignment is an efficient search strategy for finding accurate multiple alignments. The highest accuracy achieved ... Reticular Alignment can outperform ClustalW even if a very simple scoring scheme (BLOSUM62 and affine gap penalty) is ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-570
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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome | Genome Biology | Full Text
Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http:// ... memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows- ... EXACTMATCH is insufficient for short read alignment because alignments may contain mismatches, which may be due to sequencing ... Our alignment policy allows a limited number of mismatches and prefers alignments where the sum of the quality values at all ...https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure | BMC...
Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB. ... The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical ... I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic ... programming algorithms for linear sequence alignment. The new algorithm has an O(N2 log N) memory complexity, at the expense of ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-3-18
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