Tag: RefSeq

Building a Simulated Metagenomic Dataset

Building a Simulated Metagenomic Dataset – HackMD       Published Linked with GitHub — tags: ‘JPL: Genetic Inventory Project’ — # Building a Simulated Metagenomic Dataset Here we’ll create a simulated metagenomic datasets for controlled testing. This dataset was used to determine the Kraken 2 confidence score that best…

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RefSeq release 214 is available! – NCBI Insights

RefSeq release 214 is now available online, from the FTP site, and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of September 12, 2022, and contains 328,588,569 records, including 239,609,016 proteins, 47,387,931 RNAs, and sequences from 123,394 organisms. The release is provided in…

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KEGG T01001: 4171

Entry 4171              CDS       T01001                                  Symbol MCM2, BM28, CCNL1, CDCL1, D3S3194, DFNA70, MITOTIN, cdc19 Name (RefSeq) minichromosome maintenance complex component 2   KO K02540   DNA replication licensing factor MCM2 [EC:5.6.2.3] Organism hsa  Homo sapiens (human) Pathway hsa03030   DNA replication hsa04110   Cell cycle Disease H00604   Deafness, autosomal dominant Brite KEGG Orthology (KO) [BR:hsa00001] 09120 Genetic Information Processing  09124…

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KEGG T02666: 101290786

Entry 101298727         CDS       T02666                                  Name (RefSeq) triacylglycerol lipase SDP1   KO K14674   TAG lipase / steryl ester hydrolase / phospholipase A2 / LPA acyltransferase [EC:3.1.1.3 3.1.1.13 3.1.1.4 2.3.1.51] Organism fve  Fragaria vesca (woodland strawberry) Pathway fve00100   Steroid biosynthesis fve00561   Glycerolipid metabolism fve00564   Glycerophospholipid metabolism fve00565   Ether lipid metabolism fve00590   Arachidonic acid metabolism fve00591   Linoleic…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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Index of /Rsubread/annot

Name Last modified Size Description Parent Directory   –   chm13v2.0_RefSeqStri..> 2022-08-22 01:51 2.0M   chm13v2.0_RefSeq_12A..> 2022-08-22 01:51 2.5M   code/ 2022-08-22 01:53 –   hg38_RefSeqStrict_22..> 2022-08-22 01:51 2.3M   hg38_RefSeq_22Apr202..> 2022-08-22 01:51 3.0M   mm10_RefSeqStrict_22..> 2022-08-22 01:51 2.0M   mm10_RefSeq_22Jun202..> 2022-08-22 01:51 2.5M   mm39_RefSeqStrict_23..> 2022-08-22 01:51 1.9M  …

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New annotations in RefSeq – NCBI Insights

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-six new annotations in RefSeq for the following organisms: Anopheles coluzzii (mosquito) Anopheles funestus (African malaria mosquito) Astyanax mexicanus (Mexican tetra) Athalia rosae (coleseed sawfly) Bactrocera dorsalis (oriental fruit fly) Brassica napus (rape) Brienomyrus brachyistius (bony fish) Canis lupus dingo (dingo) (pictured) Caretta…

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KEGG T01015: 107278078

Entry 4330855           CDS       T01015                                  Name (RefSeq) auxin-responsive protein SAUR32   KO K14488   SAUR family protein Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa04075   Plant hormone signal transduction Brite KEGG Orthology (KO) [BR:osa00001] 09130 Environmental Information Processing  09132 Signal transduction   04075 Plant hormone signal transduction    4330855 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Auxin_inducible Motif Other DBs…

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UniProt: A0A6I9ZUN5_ACIJB

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

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Gene Set – TNFSF10

Dataset MSigDB Cancer Gene Co-expression Modules Category transcriptomics Type co-expressed gene Description tumor necrosis factor (ligand) superfamily, member 10|The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not…

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How to identify locus_tag by using RefSeq protein info (WP_*)

How to identify locus_tag by using RefSeq protein info (WP_*) 0 Hi, I would like to know the locus tag of a protein annotated with RefSeq (WP_*). For example, I would like to identify the genomic location of a protein (WP_073031595.1) and also know its adjacent proteins. The GenBank file…

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can gff2 reference used in htseq-count?

Dear all We are recently working with E.coli plasmid and tried to summarize the gene counts from our RNA-Seq samples. The short reads were mapped to E.coli plasmid using tophat which generated bam files accordingly. However, we were unable to obtain a gff3 version of our target plasmid genome, the…

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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RefSeq Release 212 is available!

RefSeq Release 212 is now available online, from the FTP site and through NCBI’s Entrezprogramming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of May 2, 2022, and contains 314,915,153 records, including 229,417,182 proteins, 44,805,833 RNAs, and sequences from 119,373 organisms. The release is provided in several directories…

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Transcription Start Site

Transcription Start Site 2 What are the best databases to check out the transcription start sites of specific genes in human genome? TSS • 130 views wget -q -O – “http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz” | gunzip -c | awk ‘(int($7)< int($8)) {if($4==”+”) {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,$7,int($7)+1,$2,$4);}else {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,int($8)-3,$8,$2,$4);}}’ chr1 69090 69091 ENST00000335137.3 + chr1 139306 139309 ENST00000423372.3…

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Summary of Fusobacterium nucleatum MJR7757B, version 26.0

Summary of Fusobacterium nucleatum, Strain MJR7757B, version 26.0 Tier 3 Uncurated Database Summary: This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Fusobacterium nucleatum MJR7757B, as obtained from RefSeq (annotation date: 04-APR-2017). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software…

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C1qBP antibody [GT1250] | Axil Scientific

This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX02847 Brand GeneTex Application IHC-PWB Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. For…

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EpCAM antibody [G8.8] | Axil Scientific

This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX80323 Brand GeneTex Application FACSICC/IFIHC-FrIPWB Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. For…

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SMAD4 antibody | Axil Scientific

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NCBI RefSeq representative and reference genomes precalculated in PhenDB

News PhenDB now contains in the “Browse” section the trait precalculations for the reference genomes and representative genomes in NCBI RefSeq. The trait prediction results can be filtered by user-specific criteria for minimal prediction confidence and minimal balanced accuracy. Three figures demonstrate the number of positive and negative predictions for…

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