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Editing and Publishing Alignments

Lecture 111. Editing and Publishing Alignments. By Ahmed Mansour Mohamed Mansour Alzohairy. Department of Genetics, Zagazig University, Zagazig, Egypt 2009. In This lecture. Reformatting your multiple sequence alignment Manually editing a multiple sequence alignment with Jalview

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Editing and Publishing Alignments

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  1. Lecture 111 Editing and Publishing Alignments By Ahmed Mansour Mohamed Mansour Alzohairy Department of Genetics, Zagazig University, Zagazig, Egypt 2009

  2. In This lecture • Reformatting your multiple sequence alignment • Manually editing a multiple sequence alignment with Jalview • Turning your Alignment into a logo • Shading a multiple sequence alignment with Boxshade

  3. You can get sample for alignment from www.tcoffee.org/dummy_aln.html.

  4. Getting Your Multiple Alignment in the Right Format • When using online servers or even local programs , you do not always have full control of what goes in and what comes out of the program you use. • - For instance, many multiple-sequence-alignment programs commonly output only one format: MSF (Multiple Sequence Format). • - What can you do if you want to analyze this multiple sequence alignment with a program that only reads FASTA-formatted alignments? The answer is simple: Use a reformatting program

  5. Note that MSF and ALN are interleaved (meaning easier for humans to read but not for machines), whereas FASTA is not

  6. Working with the right format You can request a graphic output if you want the pretty picture, but you must also keep the text version. Remember that turning a text into a graphic is always easier than the other way round!

  7. Converting formats • If the program you’re using doesn’t produce alignments in the format you need, it is possible to use a third-party conversion tool to get to the format you want. • Point your browser to (Mobyle@ Pasteur) http://mobyle.pasteur.fr/cgi-bin/portal.py

  8. Insert your email

  9. Insert sequences Only Choose Alignment format Insert Alignment Only

  10. Choose box shade to get colorful alignments Choose

  11. Along the same lines, do not take for granted that similar online servers do the same thing (even if they have the same name and the same interface). Two servers running READSEQ may run different versions of this program, or the same version with different default parameters. As a consequence, a problem that doesn’t occur with one server may occur with the next server. It really pays to keep your eyes peeled and to keep backup copies of your original files.

  12. Using Jalview to Edit Your Multiple Alignment Online

  13. To Download

  14. To Download

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