Contigs and singletons

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August undefined, 2024

WebAug 6, 2012 · BLAST searches for all contigs and singletons obtained from M. amblycephala were performed against the nr protein database using the BLASTx algorithm and an arbitrary expectation value of E −10 . Among a total 100,477 unigenes (contigs and singletons), 40,687 (40.5%) showed at least one significant alignment to an existing … WebNational Center for Biotechnology Information

EST and contig naming - USDA

WebFor the rest of the viral contigs, 469 (i.e., 66.43%) were singletons, and 77 (i.e., 10.91%) were outliers. We obtained a total of 384 VCs, of which 83 VCs contained the predicted viral contigs. Among the total predicted viral contigs, 65 contigs were associated with the RefSeq viral genomes, and 231 contigs were associated with other contigs. WebThe full-length enriched EST data were clustered and assembled into unique sequences, contigs, and singletons. The PiGenome provides functional annotation, identification of … lighthouse marine supply wilmington

What is Singletons? - SEQanswers

Web1 Dr. Julia Weiss Genetics Institute of Plant ... - Plant Physiology WebJun 1, 2024 · Reoviridae contigs/singletons found in 4 dogs were compared with reference sequence of Rotavirus A (NC_011503.2) and 3 of them covered between 10.5% and 23.4% of the VP4 gene and the other sample covered 23.6% of the VP7 gene. Furthermore, contigs/singletons matching to canine parvovirus, were found in 2 dog samples with … WebMay 18, 2012 · Several contigs and singletons were identified as CC and C-X-C motif chemokines. For the IFNs group, there was a unique contig presenting homology to D. … lighthouse marine transport

Development and genetic mapping of microsatellite markers

Annotation of RNA-seq contigs and singletons Download Table

WebSep 26, 2003 · The contigs and singletons were ordered and oriented with Bambus, a general purpose scaffolder (SOM Text). When single links were permitted, Bambus generated 522,101 scaffolds with a mean length of 3.8 kb and mean span of 8.6 kb. WebMar 16, 2010 · A combination of reference-based and de novo assemblies yielded 63,657 contigs, with 239,793 reads remaining as singletons. Based on sequence similarity with known proteins, these sequences represent approximately 17,000 unique genes, many of which are well covered by contig sequences. lighthouse maritime advisorsWebAfter the removal of poor-quality sequences, these ESTs formed 383 contigs and 1190 singletons. When all the ESTs were pooled and contigged, a total of 3754 unique sequences was identified ... peacock bedding sets queen size

"WebContigs The assembly was done by first clustering the ESTs into groups of similar sequences, using Paracel PCP. Then each cluster was separately assembled into contigs and singletons using CAP4. The contigs are named by their cluster number and their contig number within that cluster. " - Contigs and singletons

Contigs and singletons

WebDec 11, 2003 · 48 best hits (if found) represented for each contig or singleton. Normalized expectation is: (-log(exp))/100 lettuce_pfam, sunflower_pfam- results of hmmrsearch for Pfam domains in the … WebJun 18, 2015 · Over half of these sequences, 3,161 contigs and 9,389 singletons, retrieved matches from at least one related grass proteome, indicating ‘conserved’ genes among grasses . Among these, 2,555 ...

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WebDownload scientific diagram Composition of white spruce consensus sequences (contigs and singletons) according to orientation of direction of the reads (3' or 5') and according to their ... WebIn each collection, 16% of the contigs/singletons have no matches in databases and 3-5% encode hypothetical proteins; novel hypothetical proteins (not found within the female …

WebAug 17, 2016 · Total assignments for viral groups, singletons, and metagenomic viral contigs are shown above each bar. b, Phylogenetic distribution of bacterial and archaeal hosts. For each phylum a pie chart... WebJul 25, 2013 · Results. Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 …

In 1980, Staden wrote: In order to make it easier to talk about our data gained by the shotgun method of sequencing we have invented the word "contig". A contig is a set of gel readings that are related to one another by overlap of their sequences. All gel readings belong to one and only one contig, and each contig … See more A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA. In bottom-up sequencing projects, a contig refers to overlapping sequence data (reads); … See more A sequence contig is a continuous (not contiguous) sequence resulting from the reassembly of the small DNA fragments generated by bottom-up sequencing strategies. This … See more • Staden Package See more Contig can also refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical sequencing strategy is used. In this sequencing … See more • Definition of the term and historical perspective • Staden package of sequence assembly: Definitions and background information See more WebSingleton read; and; Discordant mate pairs; ... Contigs are long continuous stretch of sequence results from overlapping short reads. When you do a paired-end sequence, …

Webimage showing the five body sites with available samples. All the metagenomic viral contigs identified in each body site can be accessed from the circles in the image. (c) Table …

WebAug 14, 2024 · The genes on the contigs that were a mixture of singletons and non-singletons tended to emerge from the same species or genus. Only 8,557 (0.8%) of all mixture contigs in the oral microbiome contained potential cross-genus HGT. In the gut, there were 33,224 of these cross-genus, mixture contigs, a total of 1.8%. lighthouse markers tarkovWebLarge-scale EST sequences from C. ehrenbergii cDNA were determined (790 K sequence reads, 332 Mb), comprising 21,177 contigs and 15,299 valid singletons (Table 2).Furthermore, these contigs ... lighthouse markethttp://scorreia.com/research/singletons.pdf peacock bedroom sofaWebSep 26, 2010 · After removing redundancy, the resulting consensus sequences of contigs and singletons were again mined for GSS-SSRs for further analysis. Marker development and polymorphism detection. Primer3 software (Rozen and Skaletsky 2000) was used to design PCR primers flanking SSR sequences from the non-redundant SSR-containing … peacock bedroom designWebMay 22, 2024 · Assembled EST contigs database of C. reticulata was used to BLAST against the Citrus sinensis miRNA dataset to identify the miRNA having at least 80% identity. Both mature and precursor miRNA matches were checked out in the resultant clustered contigs and singletons to generate a consensus for the prediction of mature … peacock bedspreads and comforters lighthouse market hamiltonWebIn the context of genome assemblies, a singleton is a non-assembled read, usually a contamination or bad quality read. In gene context, it refers to a non-duplicate gene. … lighthouse market 2