emboss gui 2k81217. emboss
TRANSCRIPT
EMBOSS GUI2k81217
EMBOSS
http://bioinfo.nhri.org.tw/
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
EMBOSS GUIhttp://bioinfo.nhri.org.tw/gui/
EMBOSS GUIhttp://bioinfo.nhri.org.tw/gui/
Find programs by keywords
Find programs by keywords
html
Displays a program's help documentation manual
Additional web sites of EMBOSS
http://bioweb.pasteur.fr/seqanal/EMBOSS/
http://csc-fserve.hh.med.ic.ac.uk/emboss.html
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
Restriction Enzyme MAP
REMAP
run remap
Restriction cutting Restriction cutting sitessites
translationtranslation
Enzyme cutting Enzyme cutting frequencyfrequency
Finds and extracts open reading frames (ORFs)
GETORF
run getorf
Finds and extracts open reading frames (ORFs)
GETORF
Plot potential open reading frames
PLOTORF
run plotorf
Plot potential open reading frames
PLOTORF
Calculates fractional GC content of nucleic acid sequences
GEECEE
Calculates fractional GC content of nucleic acid sequences
GEECEE
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
Global alignment
NEEDLE
Sequence Sequence 11
Sequence Sequence 22
Global alignment
NEEDLE
Local alignmentWATER
Sequence Sequence 11
Sequence Sequence 22
Local alignmentWATER
Multiple sequence alignmentEMMA
Multiple sequence alignmentEMMA
copy
Displays a multiple sequence alignment
SHOWALIGN
Displays a multiple sequence alignment
SHOWALIGN
Identical Identical sequencesequence
Displays aligned sequences, with colouring and boxing
PRETTYPLOT
run prettyplot
• PRETTYPLOTDisplays aligned sequences, with colouring and boxing
PRETTYPLOT
http://www.ensembl.org/index.html
http://www.ensembl.org/info/website/archives/index.html
ENSMUSG00000057967
Select Ensembl database
Scans DNA sequences for transcription factors
TFSCAN
Scans DNA sequences for transcription factors
TFSCAN
http://www.cbrc.jp/research/db/TFSEARCH.html
Minus strand
Plus strand
http://www.cbil.upenn.edu/cgi-bin/tess/tess?RQ=SEA-FR-QueryS
copy & pasteagain and again
練習
試問 FGF2, FGF3, FGF4, FGF8, and FGF9 是否可被 CREB 調控？
Whole Genome Search of Candidate Genes by Profile Hidden Markove Model
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
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 ）
Searching Platform Hidden Markov Model based search tools
Promoter
EnsMart
Promotersequence
HMMER2.2g
Pattern
ClustalWCalibrate
Build
Search
KnowEREs
HMMER2.2g
ERE_DB
http://www.binfo.ncku.edu.tw/
http://thebest.binfo.ncku.edu.tw/thebest/
StAR
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
Search a PROSITE motif
PATMATMOTIFS
Search a PROSITE motif
PATMATMOTIFS
nucleic acid binding motifs
HELIXTURNHELIX
HELIXTURNHELIX
nucleic acid binding motifs
HELIXTURNHELIX
Displays membrane spanning regions
TMAP
Displays membrane spanning regions
TMAP
Homework
將序列將序列 AB009865AB009865 利用利用 EmbossEmboss 來分析來分析此序列各種特性（此序列各種特性（ ORF, ORF, restriction enzyme cutting sites, , transcription factors, motiftranscription factors, motif 等等 )) 。。請將你的結果連同說明在請將你的結果連同說明在 1212 月月 2121 日日23:59:5923:59:59 前放上你的個人網頁。前放上你的個人網頁。