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MSDB: a comprehensive, annotated database of microsatellites

2019 Nucleic Acids Research  
This is by far the most comprehensive, annotated, updated database to access and analyze microsatellite data of multiple species.  ...  MSDB (MicroSatellite DataBase) is a collection of >4 billion microsatellites from 37 680 genomes presented in a user-friendly web portal for easy, interactive analysis and visualization.  ...  ACKNOWLEDGEMENTS The authors thank Geetha Thanu, A Padmavathi, and K Ramachary from the IT section of CCMB for help in hosting the server; Phanindhar Kundurthi and Surabhi Srivastava for critical reading  ... 
doi:10.1093/nar/gkz886 pmid:31599331 pmcid:PMC6943038 fatcat:t7ebl65mvzaf7ng7h65jhodpee

Plant Molecular Biology Databases

Zubir Awan
2019 Highlights in BioScience  
Information in biological databases involves the role of genes, composition, chromosomal location, clinical impacts of mutations, and similarity of biological sequences and characteristics.  ...  We are here targeting to review and rank some of the plant databases according to their use and feature.  ...  MSDB A MSDB (Microsatellite Database) of > 650 million SSRs from 6,893 species such as archaea, fungi, bacteria, plants and animals was founded by Avvaru et al. (13) .  ... 
doi:10.36462/h.biosci.20191 fatcat:56ptwcsu7ngqljfstdfgcrvu6i

SSRome: an integrated database and pipelines for exploring microsatellites in all organisms

Morad M Mokhtar, Mohamed A M Atia
2018 Nucleic Acids Research  
Over the past decade, many databases focusing on microsatellite mining on a genomic scale were released online with at least one of the following major deficiencies: (i) lacking the classification of microsatellites  ...  In this study, we have developed 'SSRome' as a web-based, user-friendly, comprehensive and dynamic database with pipelines for exploring microsatellites in 6533 organisms.  ...  ACKNOWLEDGEMENTS The authors would like to thank the administration of Agricultural Genetic Engineering Research Institute (AGERI) as well as the administration of the Agricultural Research Center (ARC  ... 
doi:10.1093/nar/gky998 pmid:30365025 pmcid:PMC6323889 fatcat:oy4tdv6rzngglf6milnnzx2adi

Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Hongyang Wang, Yang Fu, Peng Gu, Yingying Zhang, Weilong Tu, Zhe Chao, Huali Wu, Jianguo Cao, Xiang Zhou, Bang Liu, Jennifer J. Michal, Chun Fan (+1 others)
2020 Animals  
Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of  ...  The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds.  ...  Based on the SSR-enriched library, we obtained an average of 1,225,072 SSRs in the four pig breeds, which is less than the number of SSRs in the MicroSatellite DataBase (MSDB) [54] .  ... 
doi:10.3390/ani10101792 pmid:33023098 fatcat:xdvugfwkzfdivlb5553vvnzgkq

Whole genome sequencing of metastatic colorectal cancer reveals prior treatment effects and specific metastasis features

Pauline A. J. Mendelaar, Marcel Smid, Job van Riet, Lindsay Angus, Mariette Labots, Neeltje Steeghs, Mathijs P. Hendriks, Geert A. Cirkel, Johan M. van Rooijen, Albert J. Ten Tije, Martijn P. Lolkema, Edwin Cuppen (+3 others)
2021 Nature Communications  
In addition, we identify specific genes preferentially affected by microsatellite instability.  ...  Here we present whole genome sequencing data of metastases of 429 CRC patients participating in the pan-cancer CPCT-02 study (NCT01855477).  ...  Acknowledgements We thank the Hartwig Medical Foundation, and Stichting Stelvio for Life for financial support of clinical studies and WGS analyses.  ... 
doi:10.1038/s41467-020-20887-6 pmid:33495476 fatcat:oyz5ghfcb5ad7jzunyfpmmpk6a

The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis

Xiaofeng Chi, Jiuli Wang, Qingbo Gao, Faqi Zhang, Shilong Chen
2018 Molecules  
A large number of informative repetitive sequences, including SSRs, were observed in both genomes.  ...  Here, we report the complete sequences of the chloroplast genomes of L. tibetica and L. hirsuta, which were 153,665 and 154,045 bp in length, respectively, and each included a pair of inverted repeated  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules23030602 pmid:29518967 fatcat:4orlq3gm7jfgtafv5ocu56ffnu

Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes

Magdalena Malachowicz, Roman Wenne
2019 PeerJ  
Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively.  ...  Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis.  ...  Academy of Sciences.  ... 
doi:10.7717/peerj.6245 pmid:30723611 pmcid:PMC6359903 fatcat:72vwej7z2basrg5fdhuqxtedue

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

Radka Symonová, W. Howell
2018 Genes  
This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions.  ...  Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly.  ...  Microsatellites of 31 fish species not confined to India are available in the microsatellite database MSDB [112] .  ... 
doi:10.3390/genes9020096 pmid:29443947 pmcid:PMC5852592 fatcat:wdzznsxogbheziwdpmt2mzv5xy

FusionGDB 2.0: fusion gene annotation updates aided by deep learning

Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou
FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims.  ...  A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies.  ...  ACKNOWLEDGEMENTS We thank the users of FusionGDB for valuable questions, discussions and suggestions.  ... 
doi:10.1093/nar/gkab1056 pmid:34755868 pmcid:PMC8728198 fatcat:7s6t76p25vdv7etds2dugob4xm

Investigating the Mutagenicity of Polycyclic Aromatic Compounds from the Athabasca Oil Sands Region in River Otters and a Mammalian Cell Line

Helina Gyasi, University, My
For the first objective, we used a single-molecule polymerase chain reaction (SM-PCR) assay to detect microsatellite mutations in river otters with differing liver tissue PAC concentrations in the Athabasca  ...  The objectives were: 1) to determine whether wildlife with increased exposure to PACs had increased mutations, and 2) to determine whether an anthropogenic source of PACs is mutagenic in a controlled lab  ...  Avvaru AK, Sharma D, Verma A, Mishra RK, Sowpati DT. MSDB: a comprehensive, annotated database of microsatellites. Nucleic Acids Res. 2020 Jan 8;48(D1):D155-9. 87. McCaughan F, Dear PH.  ... 
doi:10.20381/ruor-27869 fatcat:divjsvonknh6thsipk7nmlvdae


Claudius Marondedze, Claudius Marondedze
2009 unpublished
Functional genomic characterization of fruit quality traits in apple (Malus x domestica Borkh.  ...  The MASCOT tool was then used to interrogate the NCBI and MSDB databases using the mass of every peptide to identify the protein.  ...  The MASCOT search engine, using the MSDB and NCBI databases, was exploited for matching the spectra data (section 2.6.8).  ...