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Orthologous sequences
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Here we release a new version of EchinoDB, EchinoDB v2.0 (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity.
16p
vihagrid
30-01-2023
9
3
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The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs).
31p
viaristotle
29-01-2022
13
0
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Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Limited knowledge of prestin is from experiments using site-directed mutagenesis or domainswapping techniques after the amino acid residues were identified by comparing the sequence of prestin to those of its paralogs and orthologs.
11p
vijeeni2711
24-07-2021
11
0
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While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). He
9p
vijeeni2711
30-06-2021
5
1
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Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development.
12p
vilichoo2711
23-06-2021
7
1
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Bios2mds: An R package for comparing orthologous protein families by metric multidimensional scaling
The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS).
7p
viwyoming2711
16-12-2020
7
0
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Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences.
13p
vikentucky2711
26-11-2020
8
1
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Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order.
11p
vikentucky2711
24-11-2020
13
2
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High-throughput methods are generating biological data on a vast scale. In many instances, genomic, transcriptomic, and proteomic data must be interpreted in the context of signaling and metabolic pathways to yield testable hypotheses.
7p
vikentucky2711
24-11-2020
11
1
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Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions.
18p
vioklahoma2711
19-11-2020
7
1
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Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies.
10p
vioklahoma2711
19-11-2020
4
1
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Long noncoding RNAs (lncRNAs) are involved in diverse biological processes and play an essential role in various human diseases. The number of lncRNAs identified has increased rapidly in recent years owing to RNA sequencing (RNA-Seq) technology.
8p
viconnecticut2711
29-10-2020
11
1
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Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories.
12p
vicolorado2711
23-10-2020
19
1
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The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don’t code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode.
22p
vicolorado2711
22-10-2020
5
0
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Miscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding.
10p
viminato2711
22-05-2020
8
1
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Rice genome harbours many resistance genes (R-genes) with tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens like rice blast fungus M. oryzae. Nevertheless, few functional R-genes have been identified for rice blast resistance. Wild species of cultivated plants are treasure trove for important agronomic traits. The wild rice Oryza rufipogon is resistant to many virulent strains of Magnaporthe oryzae.
9p
chauchaungayxua1
04-12-2019
14
1
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We report here the full coding sequence of a novel mouse putative membrane-associated mucin containing three extracellular EGF-like motifs and a mucin-like domain consisting of at least 20 tandem repeats of 124–126 amino acids. Screening a cosmid and a BAC libraries allowed to isolate several genomic clones. Genomic and cDNA sequence comparisons showed that the gene consists of 25 exons and 24 introns covering a genomic region of 52 kb. The first intron is 16 kb in length and is followed by an unusually large exon ( 9.5 kb) encoding Ser/Thr-rich tandemly repeated sequences....
10p
system191
01-06-2013
41
2
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Mitogen activated protein kinase kinase (MKK) 3 and 6 are the main p38 mitogen-activated protein kinase activators in mammals. In the present study, three Atlantic salmon MKK6 orthologs were identified. The deduced amino acid sequences of the salmon MKK6 proteins were highly similar to mammalian MKK6 sequences, and they were ubiquitously expressed. All three were shown to be upstream activators of salmon p38.
16p
research12
29-04-2013
26
2
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Acomprehensive, structural and functional, insilicoanalysis of the medium-chain dehydrogenase/reductase (MDR) superfamily, including 583 proteins, was carried out by use of extensive database mining and theBLASTPprogram in an iterative manner to identify all known members of the superfamily. Based on phylogenetic, sequence, and func-tional similarities, the protein members of the MDR super-family were classified into three different taxonomic categories: (a) subfamilies, consisting of a closed group containing a set of ideally orthologous proteins that perform the same function;...
26p
tumor12
20-04-2013
33
3
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Prion proteins (PrP) of mammals, birds, reptiles and amphibians have been successfully cloned, expressed and purified in sufficient yields to enable 3D structure determination by NMR spectroscopy in solution. More recently, PrP ortholog genes have also been identified in several fish species, based on sequence relationships with tetrapod PrPs.
8p
media19
05-03-2013
30
1
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