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EMBOSS GUI 2k81217
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EMBOSS http://bioinfo.nhri.org.tw/
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EMBOSS Command Mode EMBOSS - functions complete - establish personal database - Unix interface JEMBOSS - HTML interface, personal account required - functions limited - java windows EMBOSS GUI - concise, easy to use - Web browser, no account needed
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EMBOSS GUI http://bioinfo.nhri.org.tw/gui/
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EMBOSS GUI http://bioinfo.nhri.org.tw/gui/
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Find programs by keywords
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html
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Displays a program's help documentation manual
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Additional web sites of EMBOSS http://bioweb.pasteur.fr/seqanal/EMBOSS/ http://csc-fserve.hh.med.ic.ac.uk/emboss.html
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Tools in EMBOSS Sequence analysis: RE MAP, ORF, translation, GC content REMAP, GETORF, PLOTORF, GEECEE Sequence alignment: NEEDLE, WATER, EMMA, SHOWALIGN, PRETTYPLAT Scans DNA sequences for transcription factors: TFSCAN Function prediction: Motif and Profiles PATMATMOTIFS Protein 2D structure: HELIXTURNHELIX TMAP
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Restriction Enzyme MAP REMAP
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Restriction cutting sites translation
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Enzyme cutting frequency
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Finds and extracts open reading frames (ORFs) GETORF
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Finds and extracts open reading frames (ORFs) GETORF
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Plot potential open reading frames PLOTORF
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Plot potential open reading frames PLOTORF
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Calculates fractional GC content of nucleic acid sequences GEECEE
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Calculates fractional GC content of nucleic acid sequences GEECEE
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Sequence alignment Global alignment: compare the whole similarity and length of two sequence NEEDLE Local alignment: find a most identical/similarity region of two sequence WATER multiple sequence alignment: EMMA, SHOWALIGN, PRETTYPLAT
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Global alignment NEEDLE Sequence 1 Sequence 2
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Global alignment NEEDLE
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Local alignment WATER Sequence 1 Sequence 2
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Local alignment WATER
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Multiple sequence alignment EMMA
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Multiple sequence alignment EMMA copy
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Displays a multiple sequence alignment SHOWALIGN
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Displays a multiple sequence alignment SHOWALIGN Identical sequence
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Displays aligned sequences, with colouring and boxing PRETTYPLOT
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Displays aligned sequences, with colouring and boxing PRETTYPLOT
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http://www.ensembl.org/index.html
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http://www.ensembl.org/info/websit e/archives/index.html
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ENSMUSG00000057967
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Select Ensembl database
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Scans DNA sequences for transcription factors TFSCAN
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Scans DNA sequences for transcription factors TFSCAN
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http://www.cbrc.jp/research/db/TFSEARCH.html
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Minus strand Plus strand
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http://www.cbil.upenn.edu/cgi-bin/tess/tess?RQ=SEA-FR- QueryS
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copy & paste again and again
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練習 試問 FGF2, FGF3, FGF4, FGF8, and FGF9 是否可被 CREB 調控?
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Whole Genome Search of Candidate Genes by Profile Hidden Markove Model
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The Binding Element Searching Tool (THE BEST) Users could build up a customized hidden markov model (HMM) via HMMER program by upload or paste a set of element sequences containing specific transcription factor binding site (in FASTA format) and use this model to search the multi-species promoter region (human, mouse and rat) retrieved from the EnsMart system annotated by ensembl project
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Motivation Search for novel regulated target genes by known transcription factor binding sites (ex. ERE) based on multiple alignments Literature search ( promoter activity 、 gel shift assay 、 ChIP )
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Searching Platform Hidden Markov Model based search tools Promoter EnsMart Promoter sequence HMMER2.2g Pattern ClustalW Calibrate Build Search Know EREs HMMER2.2g ERE_DB
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http://www.binfo.ncku.edu.tw/
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http://thebest.binfo.ncku.edu.tw/thebest/
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StAR
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練習 利用之前的練習,找出約 20 條 CRE 的 sequences (需包含 5‘ 與 3’ flanking sequences ,約 20bp 左右),以 FASTA format 輸入 THE BEST 進行分析,並找出 10 個 candidate genes
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Search a PROSITE motif PATMATMOTIFS
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Search a PROSITE motif PATMATMOTIFS
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nucleic acid binding motifs HELIXTURNHELIX
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nucleic acid binding motifs HELIXTURNHELIX
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Displays membrane spanning regions TMAP
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Displays membrane spanning regions TMAP
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Homework 將序列 AB009865 利用 Emboss 來分析此序 列各種特性( ORF,, transcription factors, motif 等 ) 。請將你的結果連同說明在 12 月 21 日 23:59:59 前放上你的個人網頁。 將序列 AB009865 利用 Emboss 來分析此序 列各種特性( ORF, restriction enzyme cutting sites, transcription factors, motif 等 ) 。請將你的結果連同說明在 12 月 21 日 23:59:59 前放上你的個人網頁。
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