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115
Pfam protein families database
- Nucleic Acids Research, 2008, 36(Database issue): D281–D288
"... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenP ..."
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Cited by 771 (13 self)
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Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metage-nomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK
HMMER web server: interactive sequence similarity searching
- Nucleic Acids Research
, 2011
"... HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the soft-ware, HMMER3, have resulted in a 100-fold speed gai ..."
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Cited by 260 (0 self)
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HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the soft-ware, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (pro-file HMM) searches via the web. A HMMER web server
Rfam: Wikipedia, clans and the ‘‘decimal’’ release
- Nucleic Acids Res
, 2011
"... The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived anno-tation. We discu ..."
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Cited by 59 (7 self)
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The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived anno-tation. We discuss the addition of groupings of related RNA families into clans and new develop-ments to the website. Rfam is available on the Web at
eggNOG v4.0: nested orthology inference across 3686 organisms
- Nucleic Acids Res
, 2014
"... With the increasing availability of various ‘omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at ..."
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Cited by 29 (6 self)
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With the increasing availability of various ‘omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at
The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages
- Nucleic Acids Res
, 2011
"... Small non-coding RNAs (sRNAs) are widespread effectors of post-transcriptional gene regulation in bacteria. Currently extensive information exists on the sRNAs of Listeria monocytogenes expressed during growth in extracellular environments. We used deep sequencing of cDNAs obtained from fractioned R ..."
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Cited by 13 (1 self)
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Small non-coding RNAs (sRNAs) are widespread effectors of post-transcriptional gene regulation in bacteria. Currently extensive information exists on the sRNAs of Listeria monocytogenes expressed during growth in extracellular environments. We used deep sequencing of cDNAs obtained from fractioned RNA (<500nt) isolated from extracellularly growing bacteria and from L. monocytogenes infected macrophages to catalog the sRNA repertoire during intracellular bac-terial growth. Here, we report on the discovery of 150 putative regulatory RNAs of which 71 have not been previously described. A total of 29 regulatory RNAs, including small non-coding antisense RNAs, are specifically expressed intracellularly. We validated highly expressed sRNAs by northern blotting and demonstrated by the construction and characterization of isogenic mutants of rli31, rli33-1 and rli50 * for intracellular expressed sRNA candi-dates, that their expression is required for efficient growth of bacteria in macrophages. All three mutants were attenuated when assessed for growth in mouse and insect models of infection. Comparative genomic analysis revealed the presence of lineage specific sRNA candidates and the absence of sRNA loci in genomes of naturally occurring infection-attenuated bacteria, with add-itional loss in non-pathogenic listerial genomes. Our analyses reveal extensive sRNA expression as an important feature of bacterial regulation during intracellular growth.
TIGRFAMs and genome properties in 2013
- Nucleic Acids Res
, 2013
"... TIGRFAMs, available online at ..."
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SUPERFAMILY 1.75 including a domain-centric gene ontology method
- Nucleic Acids Research
, 2011
"... The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 meta-genomes and other gene collections such as UniProt. All models and assignments are available to browse and downl ..."
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Cited by 12 (4 self)
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The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 meta-genomes and other gene collections such as UniProt. All models and assignments are available to browse and download at
IMG 4 version of the integrated microbial genomes comparative analysis system
- Nucl. Acids Res
"... analysis system ..."
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TreeFam v9: a new website, more species and orthology-on-the-fly
- Nucleic Acids Res
, 2014
"... TreeFam ..."
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