A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
ICDS database: interrupted CoDing sequences in prokaryotic genomes
2006
Nucleic Acids Research
Preserved Fulltext
Here, we describe the Interrupted CoDing Sequence database containing ICDS detected by a similarity-based approach in 80 complete prokaryotic genomes. ...
Unrecognized frameshifts, in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence (ICDS) that can seriously affect all subsequent steps of functional characterization, from in silico ...
All the detected ICDS are organized in the Interrupted CoDing Sequence database, accessible via a web server http://www-bio3d-igbmc.u-strasbg.fr/ICDS/. ...
doi:10.1093/nar/gkj060
pmid:16381882
pmcid:PMC1347423
fatcat:ds7b5rdfxja6lpfjmwl3bf2wya
The NADP+-isocitrate dehydrogenase gene (icd) is nitrogen regulated in cyanobacteria
1996
Journal of Bacteriology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
The two cyanobacterial icd genes show 81% sequence identity and share a typical 44-amino-acid region different from all the other icd genes sequenced so far. ...
Maximal icd mRNA accumulation was reached after 5 It of nitrogen starvation in Synechocystis cells and under dinitrogen-fixing conditions in Anabaena cells. ...
The genes coding for different IDHs have been cloned and sequenced from prokaryotic and eukaryotic sources (10, 11, 13, 19, 20, 22, 25, 26, 37, 41, 45, 53) . ...
doi:10.1128/jb.178.14.4070-4076.1996
pmid:8763933
pmcid:PMC178162
fatcat:dorf7yfsufcgnhsdlvsi4znzi4
Gramene (rice and other grasses database)
[chapter]
2008
Encyclopedia of Genetics, Genomics, Proteomics and Informatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
an organizational specialization, (6) Genome Sequence Database (GSDB): http://www.ncgr. org; interrupted sequences in prokaryotes: http:// www-bio3d-igbmc.u-strasbg.fr/ICDS/. ...
Genic sequences are richer in GC nucleotides than the non-coding tracts. In prokaryotes, introns are rare and the size of the genes is smaller. ...
Its homologs are present in prokaryotes as well as in the mitochondria of yeast, insects, and mammals. ...
doi:10.1007/978-1-4020-6754-9_7111
fatcat:dsqojxeco5gwhgpgdcm22jb33y
Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry
2016
Frontiers in Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
We validated the existence of six previously described interrupted coding sequences at the peptide level, and provide evidence for four novel frameshift positions. ...
By integrating high throughput LC/MS/MS proteomic data with genomic six frame translation and ab initio gene prediction databases, a total of 2887 ORFs were identified, including 2810 ORFs annotated to ...
Karsten Krug for fruitful discussion and help in manuscript preparation. ...
doi:10.3389/fmicb.2016.00427
pmid:27092112
pmcid:PMC4821088
fatcat:wnxyltfddnbrzifb737f2zzsny
Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?
2007
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
These interrupted coding sequences (ICDSs) may really be present in the organism or may result from misannotation based on sequencing errors. ...
We suggest that each bacterial ICDS should be investigated individually, to determine its true status and to ensure that the genome sequence is appropriate for comparative genomics analyses. ...
Such sequence errors lead to errors in annotation and comparison. An in silico survey of the published bacterial genomes shows that most contain interrupted coding sequences (ICDSs) [5] [6] [7] . ...
doi:10.1186/gb-2007-8-2-r20
pmid:17295914
pmcid:PMC1852416
fatcat:rspb237dtvberhlsb3jhxyi34a
Disrupting upstream translation in mRNAs is associated with human disease
2021
Nature Communications
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Using genetic variation from 71,702 human genomes, we assess patterns of selection in translated upstream open reading frames (uORFs) in 5'UTRs. ...
Using these variants, we map and validate gene-disease associations in two independent biobanks containing exome sequencing from 10,900 and 32,268 individuals, respectively, and elucidate their impact ...
We gratefully acknowledge the staff of the Regeneron Genetics Center for whole-exome sequencing of PMBB participants. ...
doi:10.1038/s41467-021-21812-1
pmid:33750777
fatcat:2axyyaxayzgfnipiubqzngecby
Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species
2015
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. ...
This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. ...
, ICD; complex, CX; interrupted complex, ICX; Perfect, P; interrupted perfect, IP. ...
doi:10.1371/journal.pone.0133667
pmid:26196922
pmcid:PMC4510479
fatcat:pnd6e2ihtreovoajr2q6ojcpmm
Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes
2016
Aging
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Simple sequence repeats (SSRs), or microsatellites, are tandem repeats of 1-6 bp DNA motifs [1] , which are distributed in both coding and noncoding regions of eukaryotic and prokaryotic genomes [2,3] ...
Also, some SSRs are preferentially distributed in peri-centromeric heterochromatic regions [4] and were lack of sequence conservation in centromere [5] . ...
, ICD; complex, CX; interrupted complex, ICX; Perfect, P; interrupted perfect, IP. www.aging-us.com garnettii; (2) di-> tetra-> tri-> penta-> hexanucleotide P-SSRs in the remaining nine primates; the least ...
doi:10.18632/aging.101025
pmid:27644032
pmcid:PMC5191860
fatcat:dlpa62vawzftpa62b7tau263na
Comparative Genomics of Blattabacterium cuenoti: The Frozen Legacy of an Ancient Endosymbiont Genome
2013
Genome Biology and Evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
In this study, we contribute to the investigation of the evolutionary leaps enabled by mutualistic symbioses by sequencing the genome of Blattabacterium cuenoti, primary endosymbiont of the omnivorous ...
We perform comparative analyses between the Blattabacterium cuenoti genome and that of previously sequenced endosymbionts, namely those from the omnivorous hosts the Blattella germanica (Blattelidae) and ...
Acknowledgments The sequencing service of the University of Valencia (SCSIE) is acknowledged, as well as the suggestions by two anonymous reviewers. The authors acknowledge Dr M.A. ...
doi:10.1093/gbe/evt011
pmid:23355305
pmcid:PMC3590773
fatcat:svyqygrkmbbvbkxgeeeiufs5va
Protecting sausages with bacteria instead of salt
2006
Environmental Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Furthermore, there is now a special Interrupted CoDing Sequence (ICDS) database, http:// www-bio3d-igbmc.u-strasbg.fr/ICDS/, which lists potential frameshifts. ...
The general consensus is that prokaryotic genome sequences are remarkably reliable, while eukaryotic genomes become reliable after certain manual effort. ...
doi:10.1111/j.1462-2920.2005.00985.x
pmid:16423007
fatcat:ujvf3eaoxnhhhoje6ngmcyxlvq
Traffic at the tmRNA Gene
2003
Journal of Bacteriology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
A partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmRNA gene (ssrA) than for any type of tRNA gene. ...
sequence. ...
One point of contrast is the attachment site in the protein-coding gene icd; a genomic survey of enterobacterial icd (Table 1 ) agrees with a previous study (52) , showing occupation only in some E. ...
doi:10.1128/jb.185.3.1059-1070.2003
pmid:12533482
pmcid:PMC142792
fatcat:zqvwkmcfpzeppdieyq2u7wv43q
Integrated Multi-Omic Analysis of Mycobacterium tuberculosis H37Ra Redefines Virulence Attributes
2018
Frontiers in Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Furthermore, proteogenomic analysis enabled us to identify 63 novel proteins coding genes and correct 25 existing gene models in H37Ra genome. ...
However, a recent sequencing study of H37Ra, has disproved several genomic differences earlier reported to be associated with virulence. ...
Unrecognized frameshifts, stop codons in the frame and sequencing errors lead to interrupted coding sequences (ICDS) that can seriously affect the subsequent genome analysis. ...
doi:10.3389/fmicb.2018.01314
pmid:29971057
pmcid:PMC6018540
fatcat:6bod2teqr5edtj74bewyjee3c4
Differential Gene Retention in Plastids of Common Recent Origin
2010
Molecular biology and evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
In contrast, the photosynthetic amoeba Paulinella chromatophora provides an exceptional model to study organelle evolution in a prokaryote-eukaryote (primary) endosymbiosis that occurred approximately ...
Here we sequenced the plastid genome (0.977 Mb) from the recently described Paulinella FK01 and compared the sequence with the existing data from the sister taxon Paulinella M0880/a. ...
Acknowledgments This project was partially supported by grants from the National Science Foundation Microbial Genome Sequencing program (EF 08-27023) that was awarded to H.S.Y., R.A.A., and D.B., from ...
doi:10.1093/molbev/msq032
pmid:20123796
pmcid:PMC2912470
fatcat:x6b3fqtx6vem5imj7f4j7xllo4
Genome Economization in the Endosymbiont of the Wood Roach Cryptocercus punctulatus Due to Drastic Loss of Amino Acid Synthesis Capabilities
2011
Genome Biology and Evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
In this study, the genome of Blattabacterium sp. of Cryptocercus punctulatus (BCpu) was sequenced and compared with those of the symbionts of Blattella germanica and Periplaneta americana, BBge and BPam ...
Data deposition: The complete sequences of chromosome and plasmid of Blattabacterium sp. ...
The isolated loss of argH results in an interruption of the urea cycle leaving argininosuccinate as a dead end metabolite. ...
doi:10.1093/gbe/evr118
pmid:22094859
pmcid:PMC3296467
fatcat:kclms6fklvcqxo5c7cr6cdjavi
The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
2011
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
A genome-scale reconstruction was developed and validated in order to interrogate metabolic properties. ...
Genome sequencing and automated annotation was performed by JFK and HJ. CTA did the manual curation of the annotation, comparative anlayses, and genome scale reconstruction. ...
of the Genome Encyclopedia of Microbes [153] at KRIBB for technical assistance. ...
doi:10.1186/1471-2164-12-9
pmid:21208457
pmcid:PMC3032704
fatcat:6caglopvezgpvo3meswz5xyuz4
« Previous
Showing results 1 — 15 out of 68 results