 |
English
|
正體中文
|
简体中文
|
Post-Print筆數 : 27 |
Items with full text/Total items : 116918/147948 (79%)
Visitors : 65110679
Online Users : 6046
|
|
|
Loading...
|
Please use this identifier to cite or link to this item:
https://nccur.lib.nccu.edu.tw/handle/140.119/86639
|
| Title: | Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures |
| Authors: | Chang, Jia-Ming
張家銘
Notredame, Cedric
Kemena, Carsten
Jose, Espinosa-Carrasco
Erb, Ionas
Tommaso, Paolo Di
Bussotti, Giovanni
Magis, Cedrik
Jean-Francois
Taly |
| Contributors: | 資科系 |
| Date: | 2011-11 |
| Issue Date: | 2016-04-27 15:30:09 (UTC+8) |
| Abstract: | T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when building MSAs. The series of protocols presented here show how the package can be used to multiply align proteins, RNA and DNA sequences. The protein section shows how users can select the most suitable T-Coffee mode for their data set. Detailed protocols include T-Coffee, the default mode, M-Coffee, a meta version able to combine several third party aligners into one, PSI (position-specific iterated)-Coffee, the homology extended mode suitable for remote homologs and Expresso, the structure-based multiple aligner. We then also show how the T-RMSD (tree based on root mean square deviation) option can be used to produce a functionally informative structure-based clustering. RNA alignment procedures are described for using R-Coffee, a mode able to use predicted RNA secondary structures when aligning RNA sequences. DNA alignments are illustrated with Pro-Coffee, a multiple aligner specific of promoter regions. We also present some of the many reformatting utilities bundled with T-Coffee. The package is an open-source freeware available from http://www.tcoffee.org/. |
| Relation: | Nature Protocols, 6, 1669-1682 |
| Data Type: | article |
| DOI 連結: | http://dx.doi.org/10.1038/nprot.2011.393 |
| DOI: | 10.1038/nprot.2011.393 |
| Appears in Collections: | [資訊科學系] 期刊論文
|
Files in This Item:
| File |
Description |
Size | Format | |
|---|
| index.html | | 0Kb | HTML2 | 1651 | View/Open |
|
All items in 政大典藏 are protected by copyright, with all rights reserved.
|
著作權政策宣告 Copyright Announcement1.本網站之數位內容為國立政治大學所收錄之機構典藏，無償提供學術研究與公眾教育等公益性使用，惟仍請適度，合理使用本網站之內容，以尊重著作權人之權益。商業上之利用，則請先取得著作權人之授權。
The digital content of this website is part of National Chengchi University Institutional Repository. It provides free access to academic research and public education for non-commercial use. Please utilize it in a proper and reasonable manner and respect the rights of copyright owners. For commercial use, please obtain authorization from the copyright owner in advance.
2.本網站之製作，已盡力防止侵害著作權人之權益，如仍發現本網站之數位內容有侵害著作權人權益情事者，請權利人通知本網站維護人員(
nccur@nccu.edu.tw)，維護人員將立即採取移除該數位著作等補救措施。
NCCU Institutional Repository is made to protect the interests of copyright owners. If you believe that any material on the website infringes copyright, please contact our staff(
nccur@nccu.edu.tw). We will remove the work from the repository and investigate your claim.
