Abstract：
:Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting software existed to facilitate such phylogeny inference. Hence, we developed the Peptidomes for Phylogenies (P4P) web tool, which enables the survey of similarities between microbial proteomes and simplifies the process of obtaining new biological insights into their phylogeny. P4P can be used to analyze different peptide datasets, i.e. bacteria, viruses, eukaryotic species or even metaproteomes. Also, it is able to work with whole proteome datasets and experimental mass-to-charge lists originated from mass spectrometers. The ultimate aim is to generate a valid and manageable list of peptides that have phylogenetic signal and are potentially sample-specific. Sample-to-sample comparison is based on a consensus peak set matrix, which can be further submitted to phylogenetic analysis. P4P holds great potential for improving phylogenetic analyses in challenging taxonomic groups, biomarker identification or epidemiologic studies. Notably, P4P can be of interest for applications handling large proteomic datasets, which it is able to reduce to small matrices while maintaining high phylogenetic resolution. The web server is available at http://sing-group.org/p4p.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Blanco-Míguez A,Fdez-Riverola F,Lourenço A,Sánchez Bdoi
10.1093/nar/gkx389subject
Has Abstractpub_date
2017-07-03 00:00:00pages
W265-W269issue
W1eissn
0305-1048issn
1362-4962pii
3804425journal_volume
45pub_type
杂志文章abstract：:Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA alon...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1202
更新日期：2020-02-28 00:00:00
abstract：:A tetradecanucleotide U-A-G-C(U-C-G)2G-G-C-Up corresponding to bases 21-34 of a nascent sequence of formylmethionyl tRNA of E. coli has been synthesized by the joining of two combinations of chemically synthesized oligonucleotides: 1) U-A-G-C + U-C-G-U-C-G + G-G-C-Up and 2) U-A-G-C + U-C-G-U + C-G-G-G-C-Up. In reactio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.3909
更新日期：1980-09-11 00:00:00
abstract：:MDg3 is a family of mobile dispersed genetic elements represented by 15 copies in the haploid genome of D. melanogaster and flanked, like other similar elements, by the regions of homology. In the present work, these regions of mdg3 have been sequenced. The existence of perfect direct repeats 268 base pairs long has b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.15.3263
更新日期：1980-08-11 00:00:00
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journal_title：Nucleic acids research
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更新日期：2006-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr407
更新日期：2011-09-01 00:00:00
abstract：:Poly A-containing RNA enriched in prolactin-coding sequences was isolated from female rate pituitaries after induction with diethylstilbesterol. Double stranded cDNA was synthesized from this RNA and inserted into plasmid pBR322 at the Pst I site via the poly(dG):polyy(dC) tailing method. E. coli was transformed with ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.3.915
更新日期：1979-03-01 00:00:00
abstract：:The thermal stabilities of RNA:DNA hybrids are substantially greater than those of DNA:DNA duplexes in aqueous electrolyte solutions containing high concentrations of formamide. Association rates to form DNA:DNA duplexes and DNA:RNA hybrids have been measured in these solvents. There is a temperature range in which DN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.5.1539
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.19.5765
更新日期：1982-10-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx244
更新日期：2017-05-19 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1996-09-01 00:00:00
abstract：:To examine the influence of thyrotropin (TSH) on the thyroglobulin (Tgb) mRNA content, the latter was evaluated in the cytoplasm of hog thyroid cells cultured in the absence (control cells) or presence of TSH. The Tgb mRNA levels were determined by, (i) kinetics of hybridization to sheep Tgb cDNA, (ii) capacity of cod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.10.3353
更新日期：1979-07-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg681
更新日期：2003-08-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky378
更新日期：2018-07-02 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2009-10-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1065
更新日期：2012-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr455
更新日期：2011-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm904
更新日期：2008-01-01 00:00:00
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journal_title：Nucleic acids research
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doi：10.1093/nar/gkw817
更新日期：2017-01-04 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt728
更新日期：2013-11-01 00:00:00
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更新日期：2009-02-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2014-01-01 00:00:00
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journal_title：Nucleic acids research
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doi：10.1093/nar/gkg448
更新日期：2003-07-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.11.2239
更新日期：1997-06-01 00:00:00
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更新日期：2007-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.10.4083
更新日期：1984-05-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.4.1063
更新日期：1999-02-15 00:00:00
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journal_title：Nucleic acids research
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更新日期：1997-12-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2005-05-24 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl432
更新日期：2006-07-05 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.301
更新日期：2002-01-01 00:00:00
