(Q33891354)

29 July 2017

title

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes (English)

1 reference

29 July 2017

Mark Gerstein

1 reference

29 July 2017

Nathaniel Echols

1 reference

29 July 2017

Paul Harrison

1 reference

29 July 2017

Suganthi Balasubramanian

1 reference

29 July 2017

Nicholas M Luscombe

1 reference

29 July 2017

Paul Bertone

1 reference

29 July 2017

Zhaolei Zhang

1 reference

29 July 2017

language of work or name

English

0 references

publication date

1 June 2002

1 reference

29 July 2017

published in

Nucleic Acids Research

1 reference

29 July 2017

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29 July 2017

1 reference

29 July 2017

page(s)

2515-2523

1 reference

Studying genomes through the aeons: protein families, pseudogenes and proteome evolution

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Computational inference of homologous gene structures in the human genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Genome-scale compositional comparisons in eukaryotes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Identification of thermophilic species by the amino acid compositions deduced from their genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The DNA sequence of human chromosome 21

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The genome sequence of Drosophila melanogaster

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

28 July 2018

Vertebrate pseudogenes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Interspersed repeats and other mementos of transposable elements in mammalian genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The DNA sequence of human chromosome 22

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

How representative are the known structures of the proteins in a complete genome? A comprehensive structural census

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Genome sequence of the nematode C. elegans: a platform for investigating biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Comparison of DNA sequences with protein sequences.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The complete genome sequence of Escherichia coli K-12

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Genetic and physical maps of Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

High intrinsic rate of DNA loss in Drosophila

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Analysis of compositionally biased regions in sequence databases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The evolution of proteins from random amino acid sequences. I. Evidence from the lengthwise distribution of amino acids in modern protein sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The Minimal Gene Complement of Mycoplasma genitalium

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Processed pseudogenes: characteristics and evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

A question of size: the eukaryotic proteome and the problems in defining it.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Nucleotide bias causes a genomewide bias in the amino acid composition of proteins.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

A structural census of the current population of protein sequences

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=117176

Patterns of nucleotide substitution in pseudogenes and functional genes

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12034841

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Patterns and rates of indel evolution in processed pseudogenes from humans and murids

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12034841

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/30.11.2515

1 reference

29 July 2017

1 reference

29 July 2017

1 reference