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1、三种分析蛋白结构域(Domains)的方法生物信息编程2009-09-24 23:55:50阅读1235评论0 字号：大中小订阅三种分析蛋白结构域(Domai ns)的方法1, SMART入门，蛋白结构和功能分析SMART介绍SMART (a Simple Modular Architecture Research Tool) allows the iden tificati on and anno tati on of gen etically mobile doma ins and the an alysis of doma in architectures. More tha n 500
2、 doma in families found in sig nalli ng, extracellular and chromat in-associated prote ins are detectable. These domains are extensively annotated with respect to phyletic distributions, fun cti onal class, tertiary structures and fun cti on ally importa nt residues. Each doma in found in a non-red
3、undant prote in database as well as search parameters and tax ono mic inf ormati on are stored in a relati onal database system. User in terfaces to this database allow searches for prote ins containing specific comb in ati ons of doma ins in defi ned taxa. For all the details, please refer to the p
4、ublicatio ns on SMART.SMART(http:/smart.embl-heidelberg.de/)，可以说是蛋白结构预测和功能 分析的工具集合。简单点说，就是集合了一些工具，可以预测蛋白的一些二级结 构。女口跨膜区(Transmembrane segments)，复合螺旋区(coiled coil regions)， 信号肽(Signal peptides)，蛋白结构域(PFAM domains)等。SMART前该知道的1，SMART有两种不同的模式：normal或genomic主要是用的数据库不一样。Normal SMART,用的数据库Swiss-Prot, SP-Tr
5、EMBL 和 stable Ensembl proteomes。Genomic SMART,用全基因组序 列。详细列表：http:/smart.embl-heidelberg.de/smart/list genomes.plSchultz et al. (1998) Proc. Natt. Acad. Sci. USA 95, 5857-5864LetLiriiA* H (jQM) Mjg胆皑 Auidb Re吕 32, D14NV44HOME SETUP FAO ABOUT GLOSSARY WHATS NEW FEEDBACKSMART MODE:2, 一些名词解释http:/smart.
6、embl-heidelberg.de/help/smart glossary.shtmlSMART进行时Schults et 31.0955) Proc.砧亂 /lead. Sei. UiA 95.5S57-5S6斗Lstunic et ml. C2DD8)血Aic Accds , doi: 1D. 1 D93Xh3rXgkn808H ME 5ETUF FAQ AB UT GLQS5ARY WHAT* S NEW FEEDBACK=buh4=.可以直接用各个数据库蛋白的ID。如Uniprot/Ensembl ID /Accession number (ACC)。或是直接蛋白序列。运行SMART
7、也可选择signal peptides、 PFAM domains等的预测，勾上就是。看下图SMART MODE：;NORMAL GENOMICSequence analysisYou may use either w Uniprot/Ensembl sequence identifier (ID) J accession nuiriber (ACC) or the protein sequence its elf to request the SMART service.Sequence ID or ACC(,Q8N9N1SequenceSequence SMART ResetHMhlER
8、searches of th e SMART data base occur by default. You may also Tind:utlier homologues and homologues of known sTis PFAM PROSPERO repeats Signal peptide Tra nsmembra ne Coiled coil Un structured regi ons Low complexity。另夕卜 其它不用图解显示的区域，在底下的表格也有详细说明。2, San ger的Pfam数据库网址：http:/pfam.sanger.ac.uk/目前的版本：P
9、fam 23.0 (July 2008, 10340 families)The Pfam database is a large collecti on of prote in families, each represe nted by multiple seque nee alig nments and hidde n Markov models (HMMs).Pfam 23.0 (July 2008f 10340 families)The Pfam database is a large collection of prcit曰门 familieseach represented by
10、multiple sequ alignments and hidden Markov models (HMIMs). Moi巳QUICK LIMKSVIEW A PFAM FAMILYAMALYZE YOUR PROTEIN SEQUENCE FOR PFAM MATCHThis sear 匚 h mill uis both gleba I and I 匚叵il mud els iTnerqedj and an E- liOi Ylj 匚ni 2 已七 丫口 口口牯I s =i r匚h p =ir-=i meters -a n d perform j r =i n q uf sea rch e s here Paste your protein sequence here to find mat chi 门 q Pfam f;VIEW A CLANV
