Scribd Logo
Upload

Welcome to Scribd!

  • 1K views

    Bio Edit 2008

    Uploaded by

    kumbharbajarang9092
    Bioedit is a free sequence alignment editor and analysis tool written in C++ by Tom Hall in 1997. It allows for manual and automated sequence alignments, BLAST searches, restriction mapping, translation of nucleic acids, editing of ABI trace files, and more. It works on Windows systems with at least 32MB RAM and has numerous features for editing, analyzing, and working with DNA, RNA, and protein sequences.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd

    Bio Edit 2008

    Uploaded by

    kumbharbajarang9092
    1K views26 pages
    Bioedit is a free sequence alignment editor and analysis tool written in C++ by Tom Hall in 1997. It allows for manual and automated sequence alignments, BLAST searches, restriction mapping, translation of nucleic acids, editing of ABI trace files, and more. It works on Windows systems with at least 32MB RAM and has numerous features for editing, analyzing, and working with DNA, RNA, and protein sequences.

    Copyright

    © Attribution Non-Commercial (BY-NC)

    Available Formats

    PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    Bioedit is a free sequence alignment editor and analysis tool written in C++ by Tom Hall in 1997. It allows for manual and automated sequence alignments, BLAST searches, restriction mapping, translation of nucleic acids, editing of ABI trace files, and more. It works on Windows systems with at least 32MB RAM and has numerous features for editing, analyzing, and working with DNA, RNA, and protein sequences.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    1K views26 pages

    Bio Edit 2008

    Uploaded by

    kumbharbajarang9092
    Bioedit is a free sequence alignment editor and analysis tool written in C++ by Tom Hall in 1997. It allows for manual and automated sequence alignments, BLAST searches, restriction mapping, translation of nucleic acids, editing of ABI trace files, and more. It works on Windows systems with at least 32MB RAM and has numerous features for editing, analyzing, and working with DNA, RNA, and protein sequences.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 26

    Bioedit

    Sequence alignment editor and sequence analysis tool


    http://www. mbio.ncsu.edu/BioEdit/BioEdit.html

    Chuphong  Thongnak
    Clinical Pathology, Ramathibodi Hospital

    Introduction

    3 Sequence alignment editor and sequence analysis 
    stand‐alone freeware
    3 Written by Tom Hall in 1997 using C++
    3 Version 7.0.9 last update 27/6/2007 
    Key features
    • Several modes of hand alignment
    • Automated ClustalW alignment
    • Automated Blast searches (local and WWW)
    • Plasmid drawing and annotation
    • Accessory application configuration
    • Restriction mapping
    • RNA comparative analysis tools
    • Graphical matrix data viewing tools
    • Shaded alignment figures
    • Translation‐based nucleic acid alignment
    • ABI trace viewing, editing and printing
    • Other features...

    Installation
    Requirement

    3 PC with Windows 95, 98, NT, 2000 and XP OS 
    system (Compatible with Windows Vista)

    3 A pentium with at least 32 Mb of RAM
    3 At least 30Mb free disk space
    3 Zip files extraction tools (ex. winzip, winrar, 7zip) 
    3 PDF file viewer (ex. Adobe reader, Foxit reader) 
    Duoble click “setup.exe”to start 
    installation

    In “c:\BioEdit” there is “tree32.zip”for TreeView 
    installation
    Duoble click “setup.exe”to start 
    TreeView installation

    BioEdit Alignment view
    Main Interface

    1. Menu bar 3. Sequence names
    2. Tool Bar / Speed Button 4. Sequence detail

    3 4
    Select / Slide mode:  Select residues by boxing 
    them with the mouse
    Edit mode:  You may place the cursor 
    anywhere in the document
    (except the titles) and type with 
    processor: insert and overwrite
    Grab & Drag mode:  Grab and drag a single residue 
    dynamically on the screen. Use
    the shift key to move the entire 
    sequence downstream of the 
    residue

    Lock and unlock all gaps in the entire alignment

    Locked state of above button
    When down, allows you to insert single gaps 
    by right‐clicking the mouse
    Delete gaps by right‐clicking the mouse
    Insert gaps in all sequences except the one 
    clicked on with the right mouse button
    Delete gaps in all sequences except the one 
    clicked on with the right mouse button
    Reverses the default functions of the left and 
    right mouse buttons
    Toggle “Grab & Drag” mode

    When this button is down, when sliding residues 
    is to crunch or expand downstream gaps
    When this button is down, when sliding residues is 
    to move the entire sequence downstream of the 
    selection
    Normal view mode residues are colored according to
    the current color table
    Inverse color view mode, Background boxes are 
    shaded
    “Strength of Alignment” ‐‐ Residues are shaded in 
    grayscale according to the information content at 
    each column
    Residue backgrounds are shaded according to the 
    information content at each column

    Shade residues by identity and similarity
    Draw features with sequences superimposed 
    over them

    Draw features only. Do not show sequences

    View sequences in color

    View sequences in monochrome

    Show identities to a reference sequence 
    (default = top)
    Show or hide the mutual information examiner 
    (for RNA analysis only)
    Brings up the color table edit dialog

    Toggles “ignore anchor points” mode

    Add or remove a positional marker flag

    Add or remove a column anchoring point

    Scroll speed controller

    Assign first number on ruler

    Double click  sequence name to use sequence edit 
    mode and select “Overwrite” or “Insert”
    Example 1
    Pairwise alignment for 
    checking Primer

    Go to “File > Open...” to open template and 
    primer files
    For Forward primer select template and primer 
    then go to “Sequence>Pairwise Alignment>Align 
    two sequence(allow ends to slide)

    F‐Primer anneal with template at position 
    109 ‐ 126 

    For Reverse primer select it and go to “Nucleic 
    acid>Reverse Complement” first

    TGCTTGCTTGCTGACTAT
    Reverse Complement

    ATAGTCAGCAAGCAAGCA
    Then go to “Sequence>Pairwise Alignment>Align 
    two sequence(allow ends to slide)

    R‐Primer anneal with template at position 
    270 ‐ 287 

    Go to “File > Print Alignment as Text” then you can 
    copy the alignment to other software ex. MS Word
    Example 2
    Multiple alignment And
    Creating Consensus sequence

    Open first file by Go to “File > Open...”

    Then you can open all other file by Go to “File 
    > Import > Sequence Alignment file”

    Go to “Accessory Application > ClustalW 
    Multiple alignment”
    Go to “Alignment > Create Consensus Sequence”

    Example 3
    Create Phylogenetic Guide Tree
    Open referent, out group and unknown files then 
    select all and do Multiple Alignment 

    Go to “Accessory Application > DNAmlk DNA 
    maximum Likehood program with molecular clock 
    Result show that Unknown is a member of Dengue type 4

    Example 4
    Restriction Enzyme Analysis
    Open file and then Go to “Sequence > 
    Nucleic Acid > Restrictionmap”

    Now you can save result to text file
    Example 5
    DNA Contigs Assembly

    Open file and then Go to “Accessory Application 
    > CAP contig assembly program”
    Example 6
    DNA Translation

    Open file and then Go to “Sequence> Nucleic 
    Acid> Sorted Six‐Frame Translation”
    Select Start Codon

    Result show that most possibility frame is frame 1

    Go to “Sequence> Nucleic Acid> Translate > Frame1”
    Example 7
    Amino acid Composition

    Open file and then Go to “Sequence > Protein > 
    Amino Acid Composition”
    Example 8
    ABI File Analysis

    Direct open .ABI file be Go to “File > Open...”
    then edit the sequence and save as fasta or 
    text file
    THANK YOU

    You might also like