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ExPASy数据库简介-蛋白质序列分析与预测(1)
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ExPASy数据库简介-蛋白质序列分析与预测(1) 口述：吕平江 老师 整理：林崇文、郑诗思、李佩真 1.Protein identification and characterization 4.Pattern and profile searches 5.Post-translational modification prediction 8.Secondary structure prediction 1. Protein identification and characterization蛋白质鉴定及特性描述 2. DNA -> Protein将DNA序列转为蛋白质序列的工具 3. Similarity searches相似序列的搜寻 4. Pattern and profile searches模型及图表的搜寻 5. Post-translational modification prediction预测转译时的修饰 6. Topology prediction拓朴学的预测 7. Primary structure analysis主要结构的分析 8. Secondary structure prediction次级结构预估 9. Tertiary structure三级结构 10. Sequence alignment序列比对 11. Biological text analysis生物学主题分析 说明：蛋白质体分析的工具种类繁多，以下列出在ExPASy网站中所列出的的工具及其功能中译，以灰底标示者，代表之后将举例说明使用方法。
1.Protein identification and characterization 蛋白质鉴定及特性描述 1-1 AACompIdent - Identify a protein by its amino acid composition 以胺基酸成分鉴定蛋白质。 1-2 AACompSim - Compare the amino acid composition of a Swiss-Prot entry with all other entries 比较Swiss-Prot entry与其他entries胺基酸成分分析结果的差异。 1-3 MultiIdent - Identify proteins with pI, Mw, amino acid composition, sequence tag and peptide mass fingerprinting data 以等电点、分子量、胺基酸成分、序列尾端及胜肽质谱特征资料鉴定蛋白质。 1-4 PeptIdent - Identify proteins with peptide mass fingerprinting data, pI and Mw Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in Swiss-Prot, making extensive use of database annotations 以胜肽质谱特征资料、等电点、分子量、胺基酸成分、序列尾端来鉴定蛋白质，以Swiss-Prot中所有蛋白质的理论性胜肽来比较实验上的测量以及使用者指定的胜肽质谱，提供广泛的数据库注解功能。 1-5 TagIdent - Identify proteins with pI, Mw and sequence tag, or generate a list of proteins close to a given pI and Mw 以等电点、分子量、序列尾端来鉴定蛋白质，并产生与所给之等电点及分子量最接近的蛋白质列表。 1-6 FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest. 预测可能的蛋白质转译修饰及单一胺基酸可能取代之胜肽。将实验上的胜肽质谱测量结果与指定的Swiss-Prot中的理论性胜肽或使用者所输入的序列作比较，集合其差异以作出更佳的蛋白质特性描述。 1-7 GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides) 以实验结果的质谱预测可能发生在蛋白质中的低级多糖结构。〈可免费使用并由糖蛋白中的低级多糖来加以引导〉 1-8 GlycanMass - Calculate the mass of an oligosaccharide structure 由一低级多糖蛋白的结构预测其质谱。 1-9 FindPept - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage 鉴定一由实验质谱结果所得的蛋白质胜肽，并考虑到人工的化学修饰、转译修饰(PTM)及蛋白质自体溶解等因素。 1-10 PeptideMass - Calculate masses of peptides and their post-translational modifications for a Swiss-Prot or TrEMBL entry or for a user sequence 以Swiss-Prot、TrEMBL entry或使用者所提供的序列来预测其胜肽质谱及转译时的修饰。 1-11 PeptideCutter - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence 由所提供的蛋白质序列来预测可能的蛋白质及其化学切开点。 1-12 PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK 由UMIST及 UK所提供的胜肽质谱鉴定工具。 1-13 Mascot - Peptide mass fingerprint, sequence query and MS/MS ion search from Matrix Science Ltd., London 到Matrix Science Ltd., London搜寻MS/MS离子及进行胜肽质谱鉴定。 1-14 PepSea - Protein identification by peptide mapping or peptide sequencing from Protana, Denmark 以胜肽绘图及胜肽排序来鉴定蛋白质，由Protana, Denmark提供。 1-15 PeptideSearch - Peptide mass fingerprint tool from EMBL Heidelberg 由EMBL Heidelberg所提供的胜肽质谱鉴定工具。 1-16 ProteinProspector - A variety of tools from UCSF (MS-Fit, MS-Tag, MS-Digest, etc.) for mining sequence databases in conjunction with mass spectrometry experiments [Mirrors at UCL-Ludwig, UK / Ludwig Institute Melbourne (Australia)] 一个由UCSF所提供的多样性质谱分析工具。 1-17 PROWL - Protein chemistry and mass spectrometry resource from Rockefeller and NY Universities [or from Genomic Solutions] 由Rockefeller and NY Universities提供蛋白质化学性质及质谱仪资源。 1-18 PFMUTS - Shows the possible single and double mutations of a peptide fragment from MALDI peptide mass fingerprinting 由MALDI提供，呈现一胜肽质谱鉴定及胜肽碎片可能的单一或双重变化。 1-19 CombSearch - An experimental unified interface to query several protein identification tools accessible on the web 一是试验性的蛋白质鉴定工具连结界面，相当容易在网上进入。
将DNA序列转为蛋白质序列的工具 2-1 Translate - Translates a nucleotide sequence to a protein sequence 将一DNA序列转为蛋白质序列。 2-2 Transeq - Nucleotide to protein translation from the EMBOSS package 使用EMBOSS package将核甘酸转为蛋白质 2-3 Graphical Codon Usage Analyser - Displays the codon bias in a graphical manner 以写实方法呈现密码子偏差。 2-4 BCM search launcher - Six frame translation of nucleotide sequence(s) 核甘酸序列的六种翻译结构。 2-5 Backtranslation - Translates a protein sequence back to a nucleotide sequence 将一蛋白质序列翻译回核甘酸序列。 2-6 Genewise - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors 将蛋白质的序列与基因组的DNA序列做比较，并考虑到intron及frameshifting的错误。 2-7 FSED - Frameshift error detection 侦测frameshifting的错误。 2-8 LabOnWeb - Elongation, expression profiles and sequence analysis of ESTs using Compugen LEADS clusters 使用Compugen LEADS clusters做延伸、展现图表及ESTs的序列分析。 2-9 List of gene identification software sites 列出基因鉴定的软件。 相似序列的搜寻 3-1 BLAST and WU-BLAST - Interfaces to various versions of the Basic Local Alignment Search Tool Basic Local Alignment Search工具的不同翻译连结。 3-2 BLAST Network Service on ExPASy ExPASy的BLAST Network服务器。 3-3 BLAST at EMBnet-CH/SIB (Switzerland) EMBnet-CH/SIB (Switzerland)的BLAST。 3-4 BLAST at NCBI NCBI的BLAST。 3-5 WU-BLAST at Bork's group in EMBL (Heidelberg) EMBL (Heidelberg) Bork's group的WU-BLAST。 3-6 WU-BLAST and BLAST at the EBI (Hinxton) EBI (Hinxton)的WU-BLAST及BLAST。 3-7 BLAST at PBIL (Lyon) PBIL (Lyon)的BLAST。 3-8 Bic ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator [At DKFZ or at Weizmann] 使用Bioccelerator的Bic ultra-fast rigorous (Smith/Waterman)来精确搜寻相似的序列。 3-9 MPsrch - Smith/Waterman sequence comparison at EBI 位于EBI的Smith/Waterman序列比对。 3-10 DeCypher - Smith/Waterman or FrameSearch search using the DeCypher hardware accelerator 使用DeCypher hardware accelerator的Smith/Waterman或 FrameSearch序列搜寻。 3-11 Fasta3 - FASTA version 3 at the EBI 位于EBI的FASTA version 3 3-12 FDF - Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH 位于EMBnet-CH中Paracel's Fast Data Finder (FDF)上的Smith/Waterman式搜寻。 3-13 PropSearch; searches for structural homologs using a 'properties' approach [At EMBLor at Montpellier] 使用EMBL或 Montpellier搜寻相近的结构。 3-14 SAMBA- Systolic Accelerator for Molecular Biological Applications 心缩加速装置在分子生物学上的应用。 3-15 SAWTED - Structure Assignment With Text Description 描述结构功能。 3-16 Scanps - Similarity searches using Barton's algorithm 使用Barton's algorithm搜寻相似序列。
4.Pattern and profile searches 模型及图表的搜寻 4-1 InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases 在PROSITE, Pfam, PRINTS及其他家族数据库中合并搜寻。 4-2 ScanProsite - Scans a sequence against PROSITE or a pattern against Swiss-Prot and TrEMBL 扫描一段相对于PROSITE、Swiss-Prot和TrEMBL的序列及图表。 4-3 MotifScan - Scans a sequence against protein profile databases (including PROSITE) 扫描一段相对于protein profile数据库的序列(包括PROSITE)。 4-4 Frame-ProfileScan - Scans a short DNA sequence against protein profile databases (including PROSITE) 扫描一段相对于protein profile数据库的短链DNA(包括PROSITE)。 4-5 Pfam HMM search; scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre] 在Washington University及Sanger Centre扫描一段相对于Pfam protein families db的序列(包括PROSITE)。 4-6 FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database 扫描一段相对于PRINTS Protein Fingerprint数据库的蛋白质序列。 4-7 FPAT - Regular expression searches in protein databases 蛋白质数据库中的规律表现搜寻。 4-8 PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy ] 在EBI及ExPASy产生一unaligned蛋白质的图表。 4-9 PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI 在EBI中扫描一段相对于PROSITE的序列(允许产生图解)。 4-10 PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL 在PBIL扫描一段相对于PROSITE的序列(允许错误)。 4-11 PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL 在PBIL扫描一段蛋白质序列或蛋白质数据库的图表。 4-12 SMART- Simple Modular Architecture Research Tool; at EMBL 位于EMBL的一个简单的分子结构搜寻工具。 4-13 TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM 于IBM产生一unaligned蛋白质或DNA序列的图表。 4-14 Hits - Relationships between protein sequences and motifs 蛋白质结构与motifs间的关系。
5.Post-translational modification prediction 预测转译时的修饰 5-1 SignalP - Prediction of signal peptide cleavage sites 预测信号胜 的切点。 5-2 ChloroP - Prediction of chloroplast transit peptides 叶绿体传送胜肽的预测。 5-3 MITOPROT - Prediction of mitochondrial targeting sequences 预测粒腺体的目标序列。 5-4 Predotar - Prediction of mitochondrial and plastid targeting sequences 预测粒腺体与质体的目标序列。 5-5 NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins 预测哺乳动物体内黏蛋白型态的蛋白质糖化位置。 5-6 NetNGlyc - Prediction of N-glycosylation sites in human proteins 预测人类体内的N型蛋白质糖化位置。 5-7 DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium 预测黏菌体内的O型蛋白质糖化位置。 5-8 YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences 真核生物蛋白质序列上O-beta-GlcNAc的附着位置。 5-9 big-PI Predictor - GPI Modification Site Prediction 预测GPI的修饰位置。 5-10 DGPI - Prediction of GPI-anchor and cleavage sites (Mirror site) 预测GPI的切点与接点位置(镜像站)。 5-11 NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins 真核生物蛋白质上Ser, Thr及 Tyr phosphorylation位置的预测。 5-12 NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins picornaviral proteins上切点的预测。 5-13 NMT- Prediction of N-terminal N-myristoylation N-terminal N-myristoylation的预测。 5-14 Sulfinator - Prediction of tyrosine sulfation sites 酪胺酸硫化位置的预测。 5-15 SUMOplot - Prediction of SUMO protein attachment sites SUMO蛋白质附着位置的预测。 拓朴学的预测 6-1 PSORT - Prediction of protein sorting signals and localization sites 预测蛋白质的sorting信号及localization sites。 6-2 TargetP - Prediction of subcellular location 预测次细胞的位置。 6-3 DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) 使用Dense Alignment Surface法预测原核生物的transmembrane区域。 6-4 HMMTOP- Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) 预测蛋白质的transmembrane helices (跨膜螺旋)及 拓朴学。 6-5 PredictProtein - Prediction of transmembrane helix location and topology (Columbia University) 预测蛋白质的transmembrane helices (跨膜螺旋)及 拓朴学。 6-6 SOSUI - Prediction of transmembrane regions (TUAT; Tokyo Univ. of Agriculture & Technology) 预测transmembrane区域。 6-7 TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden) 以复合序列为基础侦测Transmembrane。 6-8 TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark) 预测蛋白质的transmembrane helices (跨膜螺旋) 6-9 TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH) 预测transmembrane区域及蛋白质方位。 6-10 TopPred 2 - Topology prediction of membrane proteins (Stockholm University) 膜蛋白的拓朴学预测。
主要结构的分析 7-1 ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.) 蛋白质序列的物理及化学变量分析(胺基酸、原子结构、等电点….等) 7-2 Compute pI/Mw - Compute the theoretical pI and Mw from a Swiss-Prot or TrEMBL entry or for a user sequence 以Swiss-Prot or TrEMBL entry或使用者提供序列估算其等电点及分子量。 7-3 MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve 估算等电点及成分并可看见其滴定曲线图。 7-4 REP - Searches a protein sequence for repeats 搜寻重复的蛋白质序列。 7-5 REPRO - De novo repeat detection in protein sequences 重新侦测重复的蛋白质序列。 7-6 Radar - De novo repeat detection in protein sequences 重新侦测重复的蛋白质序列。 7-7 SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI] EMBnet-CH及EBI的蛋白质序列统计分析。 7-8 Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL] 于EMBnet-CH及 PBIL预测蛋白质的卷曲螺旋区域。 7-9 Paircoil - Prediction of coiled coil regions in proteins (Berger's method) 以Berger's法预测蛋白质的卷曲螺旋区域。 7-10 Multicoil - Prediction of two- and three-stranded coiled coils 预测蛋白质二、三级结构的卷曲螺旋。 7-11 2ZIP - Prediction of Leucine Zippers 亮氨酸拉鍊的预测。 7-12 PEST - Identification of PEST regions PEST区域的鉴定。 7-13 PESTfind - Identification of PEST regions at EMBnet Austria 以EMBnet Austria鉴定PEST的区域。 7-14 HLA_Bind - Prediction of MHC type I (HLA) peptide binding 预测MHC type I (HLA)的peptide binding。 7-15 SYFPEITHI - Prediction of MHC type I and II peptide binding 预测MHC type I及 II的 peptide binding。 7-16 ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.) 胺基酸刻度图(构造及其他参数等)。 7-17 Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence 以Hydrophobic Cluster Analysis绘出蛋白质序列。 7-18 Protein Colourer- Tool for coloring your amino acid sequence 将您的胺基酸序列上色的工具。 7-19 Three To One - Tool to convert a three-letter coded amino acid sequence to single letter code 将三码的胺基酸序列转为单一密码的工具。 7-20 Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence 将所选择的蛋白质序列以红色加以强调的工具。 7-21 HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel 蛋白质片段的环状螺旋结构模型。 7-22 RandSeq - Random protein sequence generator 随机的蛋白质序列产生器。 8.Secondary structure prediction 次级结构预估 8-1 AGADIR - An algorithm to predict the helical content of peptides 一个预估胜肽链螺旋结构的算法。 8-2 BCM PSSP - Baylor College of Medicine Baylor药物学院。 8-3 Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction 以Cascaded Multiple Classifiers进行次级结构预估。 8-4 GOR I (Garnier et al, 1978) [At PBIL or at SBDS] GOR I次级结构预估法 8-5 GOR II (Gibrat et al, 1987) GOR II次级结构预估法 8-6 GOR IV (Garnier et al, 1996) GOR IV次级结构预估法 8-7 HNN - Hierarchical Neural Network method (Guermeur, 1997) Hierarchical Neural Network次级结构预估法 8-8 Jpred - A consensus method for protein secondary structure prediction at University of Dundee Dundee大学提供的一般性次级结构预估法。 8-9 nnPredict - University of California at San Francisco (UCSF) San Francisco的California大学。 8-10 PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University Columbia大学的PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec 8-11 PSA - BioMolecular Engineering Research Center (BMERC) / Boston 波士顿分子生物学研究中心。 8-12 PSIpred - Various protein structure prediction methods at Brunel University Brunel大学所提供之多种蛋白质结构预估法。 8-13 SOPM (Geourjon and Del峄ge, 1994) SOPM次级结构预估法。 8-14 SOPMA (Geourjon and Del峄ge, 1995) SOPMA次级结构预估法。
三级结构 9-1 SWISS-MODEL - An automated knowledge-based protein modelling server 能自动化产生蛋白质模型的服务器。 9-2 Geno3d - Automatic modelling of protein three-dimensional structure 可自动产生蛋白质3D立体结构模型。 9-3 CPHmodels - Automated neural-network based protein modelling server 能自动化产生蛋白质模型的服务器。 9-4 3D-PSSM - Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit) 使用次要架构信息结合的蛋白质摺叠 1D和 3D的序列资料的识别 ( Foldfit )。 9-5 ProSup - Protein structure superimposition 蛋白质结构的叠合。 9-6 SWEET - Constructing 3D models of saccharids from their sequences 依照序列建立糖类的3D结构模型。 9-7 Swiss-PdbViewer - A program to display, analyse and superimpose protein 3D structures 可将蛋白质3D结构摺叠、分析并展示的程序。
序列比对 10-1 Binary (双重) 10-1-1 SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW 以SIM比对二序列，其结果可以LALNVIEW观看。 10-1-2 LALIGN - Finds multiple matching subsegments in two sequences 找到二序列多个相同的部分。 10-1-3 Dotlet - A Java applet for sequence comparisons using the dot matrix method 使用Java applet呈现以dot matrix method比较序列的结果。 10-2 Multiple (多重) 10-2-1 CLUSTALW [At EBI, PBIL or at EMBnet-CH] 以EBI, PBIL或EMBnet-CH比对序列。 10-2-2 T-Coffee [At EMBnet Switzerland or at CMBI] 以EMBnet Switzerland或CMBI比对序列。 10-2-3 ALIGN - at Genestream (IGH) 以Genestream (IGH)比对序列。 10-2-4 DIALIGN - Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany 德国Bielefeld大学提供的复合序列比对。 10-2-5 Match-Box - at University of Namur, Belgium 比利时Namur大学提供的复合序列比对。 10-2-6 MSA - at Washington University Washington大学提供的复合序列比对。 10-2-7 Multalin [At INRA or at PBIL] 在INRA或 PBIL比对复数序列。 10-2-8 MUSCA - Multiple sequence alignment using pattern discovery, at IBM IBM提供的pattern discovery复合序列比对。 10-2-9 AMAS - Analyse Multiply Aligned Sequences 用来分析复合序列。 10-2-10 Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building). 提升一些联合结果 (包括一致结果)的各种工具。 10-2-11 CINEMA - Color Interactive Editor for Multiple Alignments 为分析结果着色的工具。 10-2-12 ESPript - Tool to print a multiple alignment 复合序列比对结果打印工具。 10-2-13 plogo - Sequence logos at CBS/Denmark 丹麦CBS的Sequence logos。 10-2-14 GENIO/logo - Sequence logos at Stuttgart/Germany 德国Stuttgart的Sequence logos。 10-2-15 WebLogo- Sequence logos at Cambridge/UK 英国剑桥的Sequence logos。 生物学主题分析 11-1 AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts 生物医学缩写及结合字的电子数据库。 11-2 AbXtract - A prototype system for the automatic annotation of functional characteristics in protein families 蛋白质家族功能性特征自动注解系统的原型。 11-3 MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query 提供有关gene, gene-gene或 gene-drug的查询。 11-4 Protein Annotator's Assistant - A software system which assists protein annotators in the task of assigning functions to newly sequenced proteins 一个协助蛋白质注解的软件，可将最新的蛋白质序列加以分配功能。 11-5 XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE 由MEDLINE搜寻相关信息。
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