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Tytuł pozycji:

Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

Tytuł :
Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters
Autorzy :
Miao Zhenyan
Li Daofeng
Zhang Zhenhai
Dong Jiangli
Su Zhen
Wang Tao
Pokaż więcej
Temat :
Biotechnology
TP248.13-248.65
Genetics
QH426-470
Źródło :
BMC Genomics, Vol 13, Iss 1, p 60 (2012)
Wydawca :
BMC, 2012.
Rok publikacji :
2012
Typ dokumentu :
article
Opis pliku :
electronic resource
Język :
English
ISSN :
1471-2164
Relacje :
http://www.biomedcentral.com/1471-2164/13/60; https://doaj.org/toc/1471-2164
DOI :
10.1186/1471-2164-13-60
Dostęp URL :
https://doaj.org/article/03576ccff1cf4cc8bd8d384278b22021
Numer akcesji :
edsdoj.03576ccff1cf4cc8bd8d384278b22021
Czasopismo naukowe
Abstract Background Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula. Description The M. truncatula transporter database (MTDB) contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the M. truncatula Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments. Conclusions In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/.

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