*  CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments |...
... to reflect amino-acid deletions or structural divergence in the reference relative to one or more compared structures. ... for each modeled sequence, model1 was selected for further analysis. Data are shown for VP40 and sGP (Figs. 1, 2, 3); data for ... or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). ... The following sequences were downloaded from Genbank and used in this work: 1) Matrix protein (VP40) sequences for Ebolavirus ...
  https://scfbm.biomedcentral.com/articles/10.1186/s13029-015-0039-1
*  Difference between revisions of "CH391L/S13/Ancestral Sequence Reconstruction" - OpenWetWare
The amino-acid sequence in each case was determined by maximum likelihood inference from 200 extant sequences. The genes to ... experimental analysis of extinct molecules. Nature reviews. Genetics, 5(5), 366-75. doi:10. .. 1038/nrg1324]. ... Using Bayesian statistics, Risso et al. calculated the most probabilistic ancestral amino acid for each point in the sequence. ... Sequence information (Nucleic Acid and Protein) from extant species can be used to infer the sequences of common ancestor ...
  https://openwetware.org/wiki/?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=679126&oldid=678991
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
The amino-acid sequence in each case was determined by maximum likelihood inference from 200 extant sequences. The genes to ... Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet. 2004 May;5(5):366-75. DOI:10.1038/ ... Using Bayesian statistics, Risso et al. calculated the most probabilistic ancestral amino acid for each point in the sequence. ... Sequence information (Nucleic Acid and Protein) from extant species can be used to infer the sequences of common ancestor ...
  https://openwetware.org/wiki/?title=CH391L/S13/Ancestral_Sequence_Reconstruction&oldid=678930
*  Difference between revisions of "CH391L/S13/Ancestral Sequence Reconstruction" - OpenWetWare
Using Bayesian statistics, Risso et al. calculated the most probabilistic ancestral amino acid for each point in the sequence. ... Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet. 2004 May;5(5):366-75. DOI:10.1038/ ... Sequence information (Nucleic Acid and Protein) from extant species can be used to infer the sequences of common ancestor ... Sequence information (Nucleic Acid and Protein) from extant species can be used to infer the sequences of common ancestor ...
  https://openwetware.org/wiki/?title=CH391L/S13/Ancestral_Sequence_Reconstruction&curid=130605&diff=677290&oldid=677281
*  CiNii 論文 - Comparison of the Amino Acid Sequence and Phylogenetic Analysis of the Peplomer,...
Comparison of the Amino Acid Sequence and Phylogenetic Analysis of the Peplomer, Integral Membrane and Nucleocapsid Proteins of ... cDNA cloning and sequence analysis of the gene encoding the peplomer protein of feline infectious peritonitis virus. GROOT R. J ... Analysis of a 9.6 kb sequence from the 3' end fo canine coronavirus genomic RNA. HORSBURGH B. C. ... Cloning and sequence analysis of the spike gene from several feline coronaviruses. REED A. P. ...
  https://ci.nii.ac.jp/naid/10004893049
*  The primary structure of actin from rabbit skeletal muscle. Completion and analysis of the amino acid sequence - Request PDF
Completion and analysis of the amino acid sequence ... Completion and analysis of the amino acid sequence. Journal of ... Complete amino-acid sequence of actin of rabbit skeletal muscle. The complete amino-acid sequence of actin of rabbit skeletal ... A protein-chemical analysis of muscle actin differentiation. Complete amino acid sequences for four mammalian muscle actins are ... Elzinga, M., 1970: Amino acid sequence studies on rabbit skeletal muscle actin. Cyanogen bromide cleavage of the protein and ...
  https://eurekamag.com/research/006/740/006740842.php
*  Better prediction of protein contact number using a support vector regression analysis of amino acid sequence | BMC...
... each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis ... Including additional information about sequence weight and amino acid composition further improves prediction accuracies ... Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient ... In this study, we provide a more accurate contact number prediction method from protein primary sequence. We predict contact ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-248
*  Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
Direct-coupling analysis is a group of methods to harvest information about coevolving residues in a protein family by learning ... Contact map, Direct-coupling analysis, Inference, Potts model, Protein structure prediction, Pseudolikelihood National Category ...
  http://kth.diva-portal.org/smash/record.jsf?pid=diva2:752712
*  Remediated Sequence - 1FO6: CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE Sequence Report Page
Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium ... Chain A: N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE. Chain Downloadable Files. Download FASTA File. View Sequence & DSSP Image. ... Sequence Display for the Entities in PDB 1FO6 The graphical representation below shows this entry's sequences as reported in ... Sequence & Structure Relationships. Enable Jmol to view annotations in 3D.. Display Jmol. Redundancy Reduction and Sequence ...
  http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1FO6
*  Sequence Similarity - 1FO6: CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE Sequence Similarity...
Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium ... Sequence Similarity Clusters for the Entities in PDB 1FO6 Legend Entity #1 , Chains: A,B,C,D N-CARBAMoYL-D-AMINO-ACID ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Blast this sequence against all of PDB Archive.. Rank. In each cluster, the chains are sorted (i.e. ranked) according to the ...
  http://www.rcsb.org/pdb/explore/sequenceCluster.do?structureId=1FO6
*  Sequence Similarity - 1FO6: CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE Sequence Similarity...
Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium ... N-carbamyl-D-amino acid amidohydrolase 361 3.5.1.77 , Details 4 1UF7 1 A, B N-carbamyl-D-amino acid amidohydrolase 361 3.5.1.77 ... N-carbamyl-D-amino acid amidohydrolase 361 3.5.1.77 , Details 7 2GGK 1 A, B, C, D N-carbamoyl-D-amino acid amidohydrolase 358 ... N-carbamyl-D-amino acid amidohydrolase 361 3.5.1.77 , Details 2 1ERZ 1 A, B N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE 252128 3.5. ...
  http://www.rcsb.org/pdb/explore/sequenceCluster.do?structureId=1FO6&entity=1&seqid=40
*  Nutrients | Free Full-Text | Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and...
Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons ... consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found ... High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed ... Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS) and betaine-homocysteine S- ...
  http://mdpi.com/2072-6643/7/1/1
*  Polbase - Reference: Fidelity analysis of HIV-1 reverse transcriptase mutants with an altered amino-acid sequence at residues...
Fidelity analysis of HIV-1 reverse transcriptase mutants with an altered amino-acid sequence at residues Leu74, Glu89, Tyr115, ... Fidelity analysis of HIV-1 reverse transcriptase mutants with an altered amino-acid sequence at residues Leu74, Glu89, Tyr115, ...
  https://polbase.neb.com/references/9457
*  Nucleotide sequence analysis of the gene encoding the Deinococcus radiodurans surface protein, derived amino acid sequence, and...
Nucleotide sequence analysis of the gene encoding the Deinococcus radiodurans surface protein, derived amino acid sequence, and ... Base Sequence; Carbohydrates/an [Analysis]; Fatty Acids/an [Analysis]; *Genes, Bacterial; *Genes, Structural; *Gram-Positive ... Bacteria/ge [Genetics]; Membrane Lipids/an [Analysis]; Molecular Sequence Data; Protein Processing, Post-Translational; Support ... Amino acid sequence analysis of about 30% of the residues revealed that the mature polypeptide consists of at least 978 amino ...
  http://pubman.mpdl.mpg.de/pubman/faces/viewItemOverviewPage.jsp?itemId=escidoc:1582845
*  Amino acid analysis/ Nter sequencing | FRISBI
AMINO ACID ANALYSIS/ NTER SEQUENCING. Amino Acid Analysis platform:. The Amino Acid Analysis (AAA) platform at IBS provides the ... This analysis consists in hydrolyzing the sample, separating the amino acids on a cation exchange resin, and after staining, ... Amino acid sequence determination based on Edman degradation is performed using an Applied Biosystems gas-phase sequencer model ... Phenylthiohydantoin amino acid derivatives generated at each sequence cycle are identified on-line with an Applied Biosystems ...
  http://frisbi.eu/centers/instruct-centre-france-2-isbg/amino-acid-analysis-nter-sequencing/
*  IUCr) Purification, crystallization and preliminary crystallographic analysis of soybean mature glycinin A1bB2
N-terminal amino-acid sequence analysis. After the main protein bands had been excised from the SDS-PAGE gels, the proteins ... b) was subjected to N-terminal amino-acid sequence analysis. It was found that the major protein eluted in the peak at 139.1 ... X and Y indicate the fractions used for further N-terminal amino-acid sequence analysis of each protein band.. ... SDS-PAGE under reducing conditions followed by N-terminal amino-acid sequencing analyses. The fractions containing A1bB2 were ...
  http://journals.iucr.org/f/issues/2013/08/00/fw5415/index.html
*  Expression of a poriferan potassium channel: insights into the evolution of ion channels in metazoans | Journal of Experimental...
Amino acid sequence and phylogenetic analysis. Sponge inward-rectifier sequences were aligned and compared with amino acid ... To determine pairwise identity values, AmqKirA and AmqKirB amino acid sequences were each in turn aligned using LALIGN online ... The cDNAs had open reading frames of 1047 and 1071 bp, respectively, corresponding to predicted amino acid sequences of 349 and ... LALIGN global alignment of predicted amino acid sequences of two sponge inward-rectifier potassium (Kir) channels, AmqKirA and ...
  http://jeb.biologists.org/content/212/6/761
*  Sequence Similarity - 1C0K: CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE Sequence...
The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent ... Sequence Similarity Clusters for the Entities in PDB 1C0K Legend Entity #1 , Chains: A PROTEIN (D-AMINO ACID OXIDASE) protein, ... CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ...
  http://www.rcsb.org/pdb/explore/sequenceCluster.do?structureId=1C0K
*  The serpin gene family in Anopheles gambiae
3.3 Amino acid sequence comparisons and analysis. Serpins are usually formed from three β sheets (named A, B, C) and nine α- ... cDNAs of the serpins were cloned, sequenced, and complete coding sequences were generated. The amino acid sequences, were ... A multiple sequence alignment of amino acid sequences of A. gambiae serpins, human alpha-1 antitrypsin (HsA1AT), and Manduca ... 2007), but cDNA sequences we generated have improved gene models and predicted amino acid sequences for some members of the A. ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2716094/
*  Amino acid repeat data | Protein sequence analysis - OMICtools
After all, the most common way to detect repeat families so far was to manually annotate the sequence family first and only ... Many repetitions in protein sequences can be identified by using different approaches. Several repeat families have been ... amino acid sequence and amino acid composition of selected cyanobacterial proteins for further analysis. ... Amino acid repeat databases , Protein sequence analysis. A large portion of proteins contain repetitive motifs, which are ...
  https://omictools.com/amino-acid-repeat-data-category
*  Viruses | Free Full-Text | Genetic Diversity of Spike, 3a, 3b and E Genes of Infectious Bronchitis Viruses and Emergence of...
... region nucleotide sequences did not closely follow the clustering based on the S1 sequence. The New cluster 1 prevalent during ... According to phylogenetic analysis of S1 gene, the 27 isolates were divided into five genotypes, Mass, Korean-I (K-I), QX-like ... The recombination analysis revealed two new S gene recombinants, 11036 and 11052 which might have been derived from ... isolates in Korea between 1990-2011 were determined and phylogenetic and computational recombination analyses were conducted. ...
  http://www.mdpi.com/1999-4915/5/2/550/htm
*  The Identification of cDNAs That Affect the Mitosis-to-Interphase Transition in Schizosaccharomyces pombe, Including sbp1,...
Amino acid sequence analysis: A BLAST (Altschulet al. 1990) search in March 1997 using the National Center for Biotechnology ... Dark shading indicates 60% or greater amino acid identity, and light shading indicates 60% or greater amino acid similarity. ... The predicted med1p amino acid sequence is 54% identical and 67% similar to human RanBP1, and 57% identical and 70% similar to ... Amino acids are numbered in italics. The domain with highest similarity to other RanBPs is underlined. (B) Alignment of sbp1p ...
  http://www.genetics.org/content/148/2/645
*  Human enterovirus 71 subgenotype B3 lacks coxsackievirus A16-like neurovirulence in mice infection | Virology Journal | Full...
Analysis of human enterovirus 71 (EV-71) subgenotype B3 genome sequences revealed that the 3D RNA polymerase and domain Z of ... CV-A16 genome sequences were amplified from the CV-A16-infected mice brain but no amplification was obtained from all the EV-71 ... The B3 virus genome sequences had ≥85% similarity at the 3' end to CV-A16. This offers opportunities to examine if there are ... Amino acid sequence analysis. Amino acid sequences were examined after stripping the 5' UTR and 3' UTR sequences and consensus ...
  https://virologyj.biomedcentral.com/articles/10.1186/1743-422X-2-74
*  Successful herbivore attack due to metabolic diversion of a plant chemical defense | Proceedings of the National Academy of...
Amino Acid Sequence Analysis of Proteins. Protein bands were excised from Coomassie-blue-stained SDS/PAGE and native PAGE gels ... Amino acid sequencing of selected protein bands by Edman degradation confirmed the results of the LC-MS/MS analyses and ... Amino acid sequence of P. rapae NSP. A predicted extracellular targeting signal is shown in green. The protein contains two ... N-terminal amino acid sequencing by Edman degradation was performed at TopLab (Martinsried, Germany) on protein bands blotted ...
  http://www.pnas.org/content/101/14/4859
*  POSITION REQUEST
... amino acid sequence analysis; electron and immunoelectron microscopy; immunocytochemistry; biotin technology for tracing ... N-terminal sequence and mass-spectrometry analyses. Soluble Ab was associated with CSF-HDL particles of 16.8 +/- 3.2 nm in ... N-terminal sequence and mass-spectrometry analyses. Soluble Ab was associated with ~200 kDa CSF- HDL particles of 16.8 +/- 3.2 ... immunoblot analysis and enzyme-linked immunosorbent analysis. 2. Studies of DNA-hydrolysing catalytic antibodies from ...
  http://www.bio.net/bionet/mm/ageing/1996-June/002372.html