• Genes
  • Patterns of gain and loss of target genes in miR1448 miRNAs.For the four nucleotide mutations that occurred in the mature sequence of miR1448 when compared to miR482.2, poplar miR1448 lost the control of most of the target genes (miR482.2 targeted 12 NBS-LRR protein-coding genes while miR1448 only targeted 1 NBS-LRR gene). (nih.gov)
  • We collected protein sequences of 14 globin-related genes from the NCBI and reconstructed an NJ tree from an alignment with 160 amino acid sites. (nih.gov)
  • Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor. (wikipedia.org)
  • citation needed] Given their tremendous importance for biology and bioinformatics, orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences. (wikipedia.org)
  • amino acids
  • 1985) determined that human plasma beta-glycoprotein hemopexin consists of a single polypeptide chain of 439 amino acids residues with six intrachain disulfide bridges and has a molecular mass of approximately 63 kD. (wikipedia.org)
  • In order to have a homologous relationship, the sum of scores over all the aligned pairs of amino acids or nucleotides must be sufficiently high . (wikipedia.org)
  • Similarities between amino acids or nucleotides are quantified in these substitution matrices. (wikipedia.org)
  • Histogram bar heights represent the fraction of amino acids in profile columns" . (wikipedia.org)
  • The extent of the inaccuracy increases with the number of amino acids in the loop. (wikipedia.org)
  • The loop amino acids' side chains dihedral angles are often approximated from a rotamer library, but can worsen the inaccuracy of side chain packing in the overall model. (wikipedia.org)
  • In general, the most accurate predictions are for loops of fewer than 8 amino acids. (wikipedia.org)
  • Even with all these methods non-template based approaches are most accurate up to 12 residues (amino acids within the loop). (wikipedia.org)
  • Genome
  • Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. (nih.gov)
  • Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. (nih.gov)
  • Motifs
  • Within protein domains, shorter signatures known as 'motifs' are associated with particular functions, and motif databases such as PROSITE ('database of protein domains, families and functional sites') can be searched using a query sequence. (wikipedia.org)
  • Mutation
  • CS-BLAST (Context-Specific BLAST) is a tool that searches a protein sequence that extends BLAST (Basic Local Alignment Search Tool), (Basic Local Alignment Search Tool) using context-specific mutation probabilities. (wikipedia.org)
  • paralogs
  • Due to the slight sequence dissimilarity between orthologs and paralogs, it is prone to regarding paralogs as orthologs. (nih.gov)
  • Under the concept of tree reconciliation, two hemoglobin sequences of shark showed co-orthology (Figure 4a), but were identified as paralogs by Mestortho (Figure 4b).Figure 4. (nih.gov)
  • similarity
  • Significant similarity is strong evidence that two sequences are related by divergent evolution of a common ancestor. (wikipedia.org)
  • Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (wikipedia.org)
  • As with anatomical structures, high sequence similarity might occur because of convergent evolution, or, as with shorter sequences, by chance, meaning that they are not homologous. (wikipedia.org)
  • A database of known structures is searched for a loop that fits the gap of interest by similarity of sequence and stems (the edges of the gap created by the unknown loop structure). (wikipedia.org)
  • orthologous
  • Our algorithm assumes that sets of sequences exhibiting orthologous relationships are evolutionarily less costly than sets that include one or more paralogous relationships. (nih.gov)
  • The sequences within the three dotted ellipses have orthologous relationships according to previous reports. (nih.gov)
  • The α- and β-hemoglobin clusters had paraphyletic relationships due to shark hemoglobin sequences (Figure 4a), but were identified as orthologous groups by Mestortho (Figure 4b). (nih.gov)
  • substitutions
  • Although the mature sequences of miR1448 were highly homologous to the mature sequences of miR482.2, four transversional substitutions still occurred in mature miR1448 compared to mature miR482.2. (nih.gov)
  • Although four tranversional substitutions occurred, there were no transitional substitutions in the mature sequences of the MIR1448 gene. (nih.gov)
  • detection
  • This is calculated with the fraction: (pairs correctly aligned)/(pairs aligned) The graph is the benchmark Biegert and Söding used to evaluate homology detection. (wikipedia.org)
  • genomic sequence
  • The horizontal axis represents the human genomic sequence and has been annotated to show the position of the novel exon 1o, which unlike the previously recognized DNMT1 exons, shows no sequence conservation relative to mouse. (nih.gov)
  • Underlining indicates the PCR primers used for genomic sequence analysis (flanking) and double underlining for RT-PCR analysis of oocyte material. (nih.gov)
  • alignment
  • Accurate multiple sequence‐structure alignment of RNA sequences using combinatorial optimization. (currentprotocols.com)
  • The figure illustrates the sequence to sequence and profile to sequence equivalence with the alignment matrix. (wikipedia.org)
  • T-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach. (wikipedia.org)
  • It can also run and combine the output of the most common sequence and structure alignment packages. (wikipedia.org)
  • An extensive documentation is available from t_coffee_technical.htm along with a tutorial t_coffee_tutorial.htm M-Coffee a special mode of T-Coffee that makes it possible to combine the output of the most common multiple sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons, etc. (wikipedia.org)
  • Expresso and 3D-Coffee these are special modes of T-Coffee making it possible to combine sequence and structures in an alignment. (wikipedia.org)
  • List of sequence alignment software Clustal MAFFT MUSCLE ProbCons Notredame C, Higgins DG, Heringa J (2000-09-08). (wikipedia.org)
  • The problem arises often in homology modeling, where the tertiary structure of an amino acid sequence is predicted based on a sequence alignment to a template, or a second sequence whose structure is known. (wikipedia.org)
  • nucleotides
  • CCCVd have a sequence of 246 nucleotides, 44 of which are common with most viroids. (wikipedia.org)
  • Nucleotides 4 to 26 of ebv-sisRNA-1 form a short hairpin loop that presents a Uridine-rich sequence motif (a possible platform for protein interactions) into the loop. (wikipedia.org)
  • The recognition sequence and the cutting site usually match, but sometimes the cutting site can be dozens of nucleotides away from the recognition site. (wikipedia.org)
  • conservation
  • This is not to be confused with conservation in amino acid sequences, where the amino acid at a specific position has been substituted with a different one that has functionally equivalent physicochemical properties. (wikipedia.org)
  • Conservation of ebv-sisRNA sequence and secondary structure between EBV and other herpesviruses suggest shared functions in latent infection. (wikipedia.org)
  • orthologs
  • The human β-hemoglobin sequences P68871 and P68872, which showed no genetic distance to each other, were co-orthologs of P68226 (Figure 4a and b). (nih.gov)
  • Two organisms that are very closely related are likely to display very similar DNA sequences between two orthologs. (wikipedia.org)
  • Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied. (wikipedia.org)
  • 1989
  • 1989). "Regional assignment of the loci for adenylate kinase to 9q32 and for alpha 1-acid glycoprotein to 9q31-q32. (wikipedia.org)
  • genetic
  • Boxed sequences have no genetic distance between them. (nih.gov)
  • The sequences having relationships of co-orthology and no genetic distance were marked by red and blue bars, respectively. (nih.gov)
  • Four sequences of human in the cluster of myoglobin showed no genetic distance from each other (Figure 4b). (nih.gov)
  • exons
  • This gene consists of 13 exons, and alternatively spliced transcripts containing several intron sequences have been detected, but no isoforms encoded by these transcripts have been identified. (wikipedia.org)
  • query sequence
  • The development of protein domain databases such as Pfam (Protein Families Database) allow us to find known domains within a query sequence, providing evidence for likely functions. (wikipedia.org)
  • More specifically, CS-BLAST derives context-specific amino-acid similarities on each query sequence from short windows on the query sequences . (wikipedia.org)
  • Substitution matrix scores are equivalent to profile scores if the sequence profile (colored histogram) is generated from the query sequence by adding artificial mutations with the substitution matrix pseudocount scheme. (wikipedia.org)
  • regions
  • With the aim of elucidating in greater detail the genealogical origin of the present domestic fowls of the world, we have determined mtDNA sequences of the D-loop regions for a total of 21 birds, of which 12 samples belong to red junglefowl (Gallus gallus) comprising three subspecies (six Gallus gallus gallus, three Gallus gallus spadiceus, and three Gallus gallus bankiva) and nine represent diverse domestic breeds (Gallus gallus domesticus). (biomedsearch.com)
  • Homologous sequence regions are also called conserved. (wikipedia.org)
  • structure
  • The development of context-based and structure based methods have expanded what information can be predicted, and a combination of methods can now be used to get a picture of complete cellular pathways based on sequence data. (wikipedia.org)
  • 1973). "Structure of 1 -acid glycoprotein. (wikipedia.org)
  • The sequence and structure prediction of CCCVd has been documented. (wikipedia.org)
  • R-Coffee a special mode of T-Coffee making it possible to align RNA sequences while using secondary structure information. (wikipedia.org)
  • Since the loop is the least conserved portion of a protein's structure, the homology-based method cannot always find a known template that aligns with the target sequence. (wikipedia.org)
  • The remainder of the sequence is unlikely to form stable RNA structure. (wikipedia.org)
  • In addition to EBV strains, where the hairpin is ~100% conserved in sequence, this structure is also found in other lymphocrypoviruses. (wikipedia.org)
  • complete
  • For a complete list see: tclinkdb.txt T-Coffee comes along with a sophisticated sequence reformatting utility named seq_reformat. (wikipedia.org)