From its origin the Protein Information Resource (http://www-nbrf. georgetown.edu/pir/) has supported research on evolution and computational biology by designing and compiling a comprehensive, quality controlled, and well-organized protein sequence database. The database has been produced and updated on a regular schedule since 1984. Since 1988 it has been maintained collaboratively by the PIR-International, an association of data collection centers engaged in international cooperation for the development of this research resource during a period of explosive acquisition of new data. As of June 1997, essentially all sequence entries have been classified into families, allowing the efficient application of methods to propagate and standardize annotation among related sequences. The databases are available through the Internet by the World-Wide Web and FTP, or on CD-ROM and magnetic media.
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http://dx.doi.org/10.1093/nar/26.1.27 | DOI Listing |
Sci Rep
January 2025
Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
The Mycobacterium avium complex (MAC) is a group of closely related nontuberculous mycobacteria that can cause various diseases in humans. In this study, genome sequencing, comprehensive genomic analysis, and antimicrobial susceptibility testing of 66 MAC clinical isolates from King Chulalongkorn Memorial Hospital, Bangkok, Thailand were carried out. Whole-genome average nucleotide identity (ANI) revealed the MAC species distribution, comprising 54 (81.
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January 2025
Chaum Life Center, CHA University School of Medicine, Seoul, 06062, Korea.
No biomarker can effectively screen for early gastric cancer (EGC). Players in the A disintegrin and metalloproteinase (ADAM)-natural killer group 2 member D (NKG2D) receptor axis may have a role for that. As a proof-of-concept pilot study, the expression of ADAM8, ADAM9, ADAM10, ADAM12, ADAM17, and major histocompatibility complex (MHC) class I chain-related sequence A (MICA), a ligand for NKG2D, in gastric cancer was investigated in silico using The Cancer Genome Atlas (TCGA) database.
View Article and Find Full Text PDFGenomics
January 2025
Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PR China. Electronic address:
The spatiotemporal-specific gene expression is regulated by cell type-specific regulatory elements. Here we selected the H3K4me1-associated DNA sequences as candidate enhancers in two different human cell lines and performed ChIP-STARR-seq to quantify the cell-type-specific enhancer activities with high-resolution. We investigated how the activity landscape of enhancers would change when transferred from native cells (cis activity) to another cell lines (trans activity).
View Article and Find Full Text PDFPlant Sci
January 2025
Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. Electronic address:
The stripe color of watermelon is a vital commercial trait and is the focus of attention of consumers and researchers. However, the genetic determinants of watermelon stripe color are incompletely understood. Based on the results of preliminary localization studies, we constructed a large-capacity F generation population (710 plants) using light-green striped ZXG1555 and green-striped Cream of Saskatchewan (COS) watermelon strains as parental lines for fine mapping.
View Article and Find Full Text PDFBiophys Rep (N Y)
January 2025
Department of Chemistry and Biochemistry, University of California Merced, Merced, 95343; Department of Chemistry, Syracuse University, Syracuse, 13244.
Transcription factor proteins bind to specific DNA promoter sequences and initiate gene transcription. These proteins often contain intrinsically disordered activation domains (ADs) that regulate their transcriptional activity. Like other disordered protein regions, ADs do not have a fixed three-dimensional structure and instead exist in an ensemble of conformations.
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