*  CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments |...
3, box). This region is perfectly aligned at the sequence level, yet displays poor structural homology when examined using ... 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 ... CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments. ...
  https://scfbm.biomedcentral.com/articles/10.1186/s13029-015-0039-1
*  "Large Grain Size Stochastic Optimization Alignment" by Hyrum Carroll, Mark J. Clement et al.
Large Grain Size Stochastic Optimization Alignment (LGA) exploits the relationship between phylogenies and multiple sequence ... quality of guide trees used for computation of multiple sequence alignments and eliminating computation of multiple sequence ... wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain ... DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ...
  https://scholarsarchive.byu.edu/facpub/291/
*  free sequence homology search on WWW
... Juergen Brosius RNA.world at uni-muenster.de Sun Mar 31 03:53:13 EST 1996 *Previous ... Please call it sequence SIMILARITY In a search you may find many sequence similarities but only few of the matches may ... 1987) Homology in proteins and nucleic acids: A terminology muddle and a way out of it. Cell 60, 667 *Previous message: free ...
  http://www.bio.net/bionet/mm/bioforum/1996-March/019073.html
*  'sequence homology' Protocols and Video...
... sequence homology' include 'Genetic Manipulation in Δku80 Strains for Functional Genomic Analysis of Toxoplasma gondii', ' ... Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models', 'Identification of ... Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS', 'Targeted in Situ Mutagenesis of ... Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples', 'Quantitation and Analysis of the ...
  https://www.jove.com/keyword/sequence+homology
*  Amino Acid Sequence Homology - Medical Dictionary online-medical-dictionary.org
Amino Acid Sequence Homology. The degree of similarity between sequences of Amino Acids. This information is useful for the ...
  http://www.online-medical-dictionary.org/definitions-a/amino-acid-sequence-homology.html
*  Sequence homology - Wikipedia
Sequence homology is the biological homology between protein or DNA sequences, defined in terms of shared ancestry in the ... Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. The term "percent homology ... "quantify the homology". Based on the definition of homology specified above this terminology is incorrect since sequence ... Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. Such partial ...
  https://en.wikipedia.org/wiki/Sequence_homology
*  Sequence Similarity - 1F5X: NMR STRUCTURE OF THE Y174 AUTOINHIBITED DBL HOMOLOGY DOMAIN Sequence Similarity Report...
Structural basis for relief of autoinhibition of the Dbl homology domain of proto-oncogene Vav by tyrosine phosphorylation. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1F5X Legend Entity #1 , Chains: A RHO-GEF VAV protein, length: 208 (BLAST ... 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=1F5X
*  The American Journal of Tropical Medicine and Hygiene | Repeated Immunogenic Amino Acid Sequences of Plasmodium Species Share...
By reducing homologies of such peptide vaccines to host proteins, the possibility of autoimmune complications may be reduced, ... amino acid sequences between tandemly repeated Plasmodium amino acid sequences and the human and human viral sequences compiled ... Matches of at least 4 amino acids were found for all sequences. In the database, 29 matches were found for human proteins and ... Six published repetitive immunogenic amino acid sequences from the circumsporozoite (CS) antigen, ring-infected erythrocyte ...
  http://www.ajtmh.org/content/journals/10.4269/ajtmh.1987.37.258
*  A Mechanism for RecA-Promoted Sequence Homology Recognition and Strand Exchange Between Single-Stranded DNA and Duplex DNA,...
p>A central function of RecA protein during homologous recombination is to promote sequence recognition and strand exchange ... A Mechanism for RecA-Promoted Sequence Homology Recognition and Strand Exchange Between Single-Stranded DNA and Duplex DNA, via ... Preliminary calculations suggest that sequence homology recognition within the triplex of association is partial and that it is ... A central function of RecA protein during homologous recombination is to promote sequence recognition and strand exchange ...
  http://www.jbsdonline.com/a-mechanism-reca-promoted-sequence-homology-recognition-and-strand-exchange-between-single-stranded-dna-and-duplex-dna-via-triple-helical-intermediates-p10048.html
*  Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence...
Search for non-mutually exclusive exons sharing similar length, same reading frame, and sequence homology. It could well be ... False negatives are those exons that do not meet the preconditions of similar length and sequence homology. However, if those ... The query exon and the candidate exon have identical lengths and show strong homology. Based on the multiple sequence alignment ... In total, 94 exons of similar length, same splice sites and reading frames, and sequence homology have been identified by ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-270
*  Sequence Similarity - 1AWE: HUMAN SOS1 PLECKSTRIN HOMOLOGY (PH) DOMAIN, NMR, 20 STRUCTURES Sequence Similarity Report...
A possible structural role for the sequential association of diffuse B cell lymphoma and pleckstrin homology domains. ... The solution structure of the pleckstrin homology domain of human SOS1. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1AWE Legend Entity #1 , Chains: A SOS1 protein, length: 130 (BLAST) ...
  http://www.rcsb.org/pdb/explore/sequenceCluster.do?structureId=1AWE
*  Human prostatic acid phosphatase: cDNA cloning, gene mapping and protein sequence homology with lysosomal acid phosphatase. -...
Human prostatic and lysosomal acid phosphatases exhibit 50% sequence homology, including five Cys residues and two putative N- ... The complete sequence of 354 amino acids for the mature enzyme was determined by sequencing both cDNA and protein. ... A dimer and a monomer of the conserved Alu-repeats are present in the longer 3' noncoding sequences. ... Human prostatic acid phosphatase: cDNA cloning, gene mapping and protein sequence homology with lysosomal acid phosphatase.. * ...
  https://www.semanticscholar.org/paper/Human-prostatic-acid-phosphatase-cDNA-cloning-gene-Sharief-Lee/be9566abd89d895d6cf7d92a5751e45623bd4989
*  Opriessnig T. 2005;13(5):246-253. Genomic homology of ORF 5 gene sequence between modified live vaccine virus and porcine...
Genomic homology of ORF 5 gene sequence between modified live vaccine virus and porcine reproductive and respiratory syndrome ... Genomic homology of ORF 5 gene sequence between modified live vaccine virus and porcine reproductive and respiratory syndrome ... sequencing of open reading frame (ORF) 5, these three isolates vary considerably from each other (72% to 86% homology) and from ... Genetic sequencing remains a useful epidemiological tool for determining whether a field isolate may be a derivative of an MLV ...
  https://www.aasv.org/shap/issues/v13n5/v13n5p246.html
*  Dihydrofolate Reductase: Partial Sequence of the Lactobacillus casei Enzyme and Homology with other Dihydrofolate Reductases |...
Dihydrofolate Reductase: Partial Sequence of the Lactobacillus casei Enzyme and Homology with other Dihydrofolate Reductases. ... Dihydrofolate Reductase: Partial Sequence of the Lactobacillus casei Enzyme and Homology with other Dihydrofolate Reductases ... Dihydrofolate Reductase: Partial Sequence of the Lactobacillus casei Enzyme and Homology with other Dihydrofolate Reductases ... Dihydrofolate Reductase: Partial Sequence of the Lactobacillus casei Enzyme and Homology with other Dihydrofolate Reductases ...
  http://www.biochemsoctrans.org/content/5/4/1097
*  Sequence Similarity - 1BMX: HIV-1 CAPSID PROTEIN MAJOR HOMOLOGY REGION PEPTIDE ANALOG, NMR, 8 STRUCTURES Sequence...
... capsid protein major-homology-region peptide analogs by NMR spectroscopy. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1BMX Legend Entity #1 , Chains: A HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 ... 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=1BMX
*  OPUS at UTS: Discovery of an MIT-like atracotoxin family: spider venom peptides that share sequences homology but not...
These peptides all show significant amino acid sequence homology to atracotoxin-Hvf17 (ACTX-Hvf17), a non-toxic peptide ... These peptides all show significant amino acid sequence homology to atracotoxin-Hvf17 (ACTX-Hvf17), a non-toxic peptide ... Discovery of an MIT-like atracotoxin family: spider venom peptides that share sequences homology but not pharmacological ... Discovery of an MIT-like atracotoxin family: spider venom peptides that share sequences homology but not pharmacological ...
  https://opus.lib.uts.edu.au/handle/10453/593
*  Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families - Current Protocols
... sequences identified in a wide variety of organisms ... Homology search with fragmented nucleic acid sequence patterns ... sequences, using manually curated sequence alignments to build powerful statistical models of sequence and structure ... Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. ... ncRNA presents a challenge for homology detection, as the primary sequence is often poorly conserved and de novo secondary ...
  http://www.currentprotocols.com/WileyCDA/CPUnit/refId-bi1213.html?quicktabs_cp=cited
*  Gap junction - Wikipedia
Innexins have no significant sequence homology with connexins.[8] Though differing in sequence to connexins, innexins are ... C. elegans Sequencing, Consortium (Dec 11, 1998). "Genome sequence of the nematode C. elegans: a platform for investigating ... based on gene mapping and sequence similarity: A, B and C (for example, GJA1, GJC1).[16][17][18] However, connexin genes do not ... with an amino acid sequence similar to innexins[13]), in fact functions as a single-membrane channel that communicates with the ...
  https://en.wikipedia.org/wiki/Gap_junction
*  Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile - Dicty cDB ...
... amino acid sequence and results of homology search), and expression profile ... Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile Data detail ... EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence by the assembly program Phrap (http ... Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile. ...
  https://dbarchive.biosciencedbc.jp/en/dicty-cdb/data-2.html
*  Multiple Alignment
Aligning DNA sequences: homology and phylogenetic weighting. in M. J. Miyamoto and J. Cracraft, eds. Phylogenetic Analysis of ... Sequences that are aligned to each other first are more likely to group closer to each other in resulting phylogenies simply as ... One method would be to simply align them in the order that they appear in the unaligned sequence-containing file as is done in ... In the first place, sequences are long and one needs an efficient way to discover where indels are. For two taxa this can be ...
  http://research.amnh.org/~siddall/methods/align.html
*  Plus it
Sequence Homology Search.. CTT homologues were searched with BLASTP 1.4.11 MP, using strategy (identity matrix, word size one, ... The third peptide was the CTT homologue CLP, found by sequence homology search from SWISS-PROT and EMBL databases by Blast 1.4. ... Furthermore, the CTT sequence does not resemble known cell-binding sequences of laminin (51) . On the other hand, the fact that ... Our query sequence was CXXHWGFTXC. Nine analogues were found, among them a part of the EGF-7 domain in human laminin β-1 chain ...
  http://cancerres.aacrjournals.org/content/61/10/3978
*  IJMS | Free Full-Text | Transcriptomic Analysis in Diabetic Nephropathy of Streptozotocin-Induced Diabetic Rats | HTML
Analysis of Sequence Homology of EST's. EST's, based on their differential expression pattern, were selected and sequenced. The ... The products were sequenced and subject to homology search by using BLAST program at the web site of National Center of ... Although several EST's showed homology with genes whose function could suggest a possible role in the pathogenesis of DN, ... As aforementioned, based on hybridization signals, 160 EST's were selected for sequencing, from which 72 were down- and 88 over ...
  http://www.mdpi.com/1422-0067/12/12/8431/htm
*  Recombination between adenovirus type 12 DNA and a hamster preinsertion sequence in a cell-free system. Patch homologies and...
The patchy homologies are similar to those found earlier during the analyses of some of the junction sequences in integrated ... Recombination between adenovirus type 12 DNA and a hamster preinsertion sequence in a cell-free system. Patch homologies and ... Recombination between adenovirus type 12 DNA and a hamster preinsertion sequence in a cell-free system. Patch homologies and ... striking patchy homologies have been observed between the p7 and Ad12 junction sequences, and between Ad12 DNA or p7 DNA and ...
  http://www.biochemie.abi.med.uni-muenchen.de/publications/article/pub_1992_007.html
*  IUCr) Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface
Sequence homology is based on the full-length amino-acid sequences of ChlV-Lig and T7-Lig and the ligase domain of Mtu-Lig ( ... Sequence homology (E-value). Length. R.m.s.d. (Å). Aligned SSEs. Z-score. Length. R.m.s.d. (Å). Aligned SSEs. Z-score. ... and homology searches against the nonredundant protein sequences database. SignalP 4.1 (Gram-negatives networks setting, D ... Sequence homology with other putatively periplasmic, minimal-type bacterial ADLs suggests that the lack of loop regions could ...
  http://journals.iucr.org/d/issues/2014/11/00/rr5081/index.html
*  The Role of Two F-Box Proteins, SLEEPY1 and SNEEZY, in Arabidopsis Gibberellin Signaling | Plant Physiology
Sequence Homology of SLY1 and SNE/SLY2. The homology of SLY1 to SNE is diagrammed in Figure 1 at both the level of mRNA and ... Domain structure and homology of the SLY1 and SNE genes and predicted protein sequences. A, Gene structure of two F-box ... amino acid sequence homology. The N-terminal domains before the F-box domain (SLY1, amino acids 1-32; SNE, 1-24) have 55.4% DNA ... amino acid homology; the F-box domain itself (SLY1, amino acids 32-77; SNE, 25-72) has 55.0% DNA/26.8% amino acid homology; and ...
  http://www.plantphysiol.org/content/155/2/765?ijkey=c6be75d3c98b378e78070a4a600ab36a49376b02&keytype2=tf_ipsecsha