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ICDS database: interrupted CoDing sequences in prokaryotic genomes

E. Perrodou
2006 Nucleic Acids Research  
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

M I Muro-Pastor, J C Reyes, F J Florencio
1996 Journal of Bacteriology  
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  
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

Matthys G. Potgieter, Kehilwe C. Nakedi, Jon M. Ambler, Andrew J. M. Nel, Shaun Garnett, Nelson C. Soares, Nicola Mulder, Jonathan M. Blackburn
2016 Frontiers in Microbiology  
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?

Caroline Deshayes, Emmanuel Perrodou, Sebastien Gallien, Daniel Euphrasie, Christine Schaeffer, Alain Van-Dorsselaer, Olivier Poch, Odile Lecompte, Jean-Marc Reyrat
2007 Genome Biology  
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

David S. M. Lee, Joseph Park, Andrew Kromer, Aris Baras, Daniel J. Rader, Marylyn D. Ritchie, Louis R. Ghanem, Yoseph Barash
2021 Nature Communications  
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

Wen-Hua Qi, Xue-Mei Jiang, Lian-Ming Du, Guo-Sheng Xiao, Ting-Zhang Hu, Bi-Song Yue, Qiu-Mei Quan, Ulrike Gertrud Munderloh
2015 PLoS ONE  
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

Wen-Hua Qi, Chao-chao Yan, Wu-Jiao Li, Xue-Mei Jiang, Guang-Zhou Li, Xiu-Yue Zhang, Ting-Zhang Hu, Jing Li, Bi-Song Yue
2016 Aging  
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

Rafael Patiño-Navarrete, Andrés Moya, Amparo Latorre, Juli Peretó
2013 Genome Biology and Evolution  
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

Michael Y. Galperin
2006 Environmental Microbiology  
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

K. P. Williams
2003 Journal of Bacteriology  
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

Sneha M. Pinto, Renu Verma, Jayshree Advani, Oishi Chatterjee, Arun H. Patil, Saketh Kapoor, Yashwanth Subbannayya, Remya Raja, Sheetal Gandotra, T. S. Keshava Prasad
2018 Frontiers in Microbiology  
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

A. Reyes-Prieto, H. S. Yoon, A. Moustafa, E. C. Yang, R. A. Andersen, S. M. Boo, T. Nakayama, K.-i. Ishida, D. Bhattacharya
2010 Molecular biology and evolution  
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

Alexander Neef, Amparo Latorre, Juli Peretó, Francisco J. Silva, Miguel Pignatelli, Andrés Moya
2011 Genome Biology and Evolution  
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

Colin T Archer, Jihyun F Kim, Haeyoung Jeong, Jin Hwan Park, Claudia E Vickers, Sang Yup Lee, Lars K Nielsen
2011 BMC Genomics  
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
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