Category: VDB

SRA Toolkit Error while using prefetch

SRA Toolkit Error while using prefetch 1 After installing SRA-toolkit I downloaded an SRA file and when I tried to download another SRA file then it gave me the following error: prefetch:` symbol lookup error: /lib/x86_64-linux-gnu/libncbi-vdb.so.2: undefined symbol: vdb_mbedtls_md_setup How to fix this? sra-toolkit • 20 views • link •…

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KEGG ENZYME: 6.3.2.6

Entry EC 6.3.2.6                  Enzyme                                  Name phosphoribosylaminoimidazolesuccinocarboxamide synthase;phosphoribosylaminoimidazole-succinocarboxamide synthetase;PurC;SAICAR synthetase;4-(N-succinocarboxamide)-5-aminoimidazole synthetase;4-[(N-succinylamino)carbonyl]-5-aminoimidazole ribonucleotide synthetase;SAICARs;phosphoribosylaminoimidazolesuccinocarboxamide synthetase;5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase Class Ligases;Forming carbon-nitrogen bonds;Acid-D-amino-acid ligases (peptide synthases)BRITE hierarchy Sysname 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming) Reaction(IUBMB) ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate [RN:R04591] Reaction(KEGG) Substrate ATP [CPD:C00002]; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate [CPD:C04751]; L-aspartate [CPD:C00049] Product ADP [CPD:C00008]; phosphate…

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KEGG ENZYME: 3.1.3.89

Entry EC 3.1.3.89                 Enzyme                                  Name 5′-deoxynucleotidase;yfbR (gene name) Class Hydrolases;Acting on ester bonds;Phosphoric-monoester hydrolasesBRITE hierarchy Sysname 2′-deoxyribonucleoside 5′-monophosphate phosphohydrolase Reaction(IUBMB) a 2′-deoxyribonucleoside 5′-monophosphate + H2O = a 2′-deoxyribonucleoside + phosphate [RN:R10776] Reaction(KEGG) Substrate 2′-deoxyribonucleoside 5′-monophosphate [CPD:C00676]; H2O [CPD:C00001] Product Comment The enzyme, characterized from the bacterium Escherichia coli, shows strict specificity towards…

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KEGG ENZYME: 3.6.1.22

Entry EC 3.6.1.22                 Enzyme                                  Name NAD+ diphosphatase;NPY1 (gene name);nudC (gene name);NUDT7 (gene name);nicotinamide adenine dinucleotide pyrophosphatase;NADP pyrophosphatase;NADH pyrophosphatase;NAD+ phosphohydrolase Class Hydrolases;Acting on acid anhydrides;In phosphorus-containing anhydridesBRITE hierarchy Sysname NAD(H) phosphohydrolase Reaction(IUBMB) Reaction(KEGG) Substrate Product Comment This enzyme, described from plants, animals, and bacteria, can act on both reduced and oxidized forms of…

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KEGG ENZYME: 2.6.1.52

Entry EC 2.6.1.52                 Enzyme                                  Name phosphoserine transaminase;PSAT;phosphoserine aminotransferase;3-phosphoserine aminotransferase;hydroxypyruvic phosphate-glutamic transaminase;L-phosphoserine aminotransferase;phosphohydroxypyruvate transaminase;phosphohydroxypyruvic-glutamic transaminase;3-O-phospho-L-serine:2-oxoglutarate aminotransferase;SerC;PdxC;3PHP transaminase Class Transferases;Transferring nitrogenous groups;TransaminasesBRITE hierarchy Sysname O-phospho-L-serine:2-oxoglutarate aminotransferase Reaction(IUBMB) (1) O-phospho-L-serine + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate [RN:R04173]; (2) 4-phosphooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate [RN:R05085] Reaction(KEGG) Substrate O-phospho-L-serine [CPD:C01005]; 2-oxoglutarate [CPD:C00026]; 4-phosphooxy-L-threonine [CPD:C06055] Product…

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Is a variant worse than Delta on the way? Viral evolution offers clues.

Somewhere in India last October, a person—likely immunocompromised, perhaps taking drugs for rheumatoid arthritis or with an advanced case of HIV/AIDS—developed COVID-19. Their case might have been mild, but because of their body’s inability to clear the coronavirus it lingered and multiplied. As the virus replicated and moved from one…

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Bioconductor – traviz (development version)

DOI: 10.18129/B9.bioc.traviz     This is the development version of traviz; to use it, please install the devel version of Bioconductor. Trajectory functions for visualization and interpretation. Bioconductor version: Development (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in…

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KEGG ENZYME: 1.14.12.17

Entry EC 1.14.12.17               Enzyme                                  Name nitric oxide dioxygenase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donorBRITE hierarchy Sysname nitric oxide,NAD(P)H:oxygen oxidoreductase Reaction(IUBMB) 2 nitric oxide + 2 O2 + NAD(P)H =…

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blastn_vdb Error: Cannot open VDB:

blastn_vdb Error: Cannot open VDB: 0 I’m working locally with sra-toolkit. I have downloaded a sra files, validate it with vdb-validate and when I try to do a search with blastn-dbd the following error occurs Error: Cannot get VDB column: ./SRR7443983.sra.SEQUENCE.ACC_PREFIX Anyone knows how to fix it? Thanks blastn_vdb •…

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Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )

Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles ) 1 I’m trying to achieve what this post was looking for Add Dp Tag To Genotype Field Of Vcf File Currently this is my command: bcftools mpileup -Ou –max-depth 8000 –min-MQ…

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VcfSampleCompare – empty output with warnings

Hello to all, I have 10 vcf files – 5 female fish and 5 male fish, I have merged all 10 fish to one vcf file.(all_fish.vcf) I performed the VcfSampleCompare analysis on ‘all_fish.vcf’ , following this:github.com/hepcat72/vcfSampleCompare The example command : vcfSampleCompare.pl –sample-group ‘wt1 wt2 wt3’ –sample-group ‘mut1 mut2 mut3’ input.vcf…

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