Fu Berlin Dissertation Latex

Submission Format Guidelines for Doctoral theses or Habilitation treatises


Use these pages as a guide to set up the format of your dissertation, thesis, or habilitation for electronic submission. In these pages the word “dissertation” also includes theses and habilitations. There are several steps in the submission process, which we will walk you through and explain how to generate the files. For information about formal requirements please refer to Online submission of Doctoral theses or Habilitation treatises.

If you need assistance you are welcome to contact the editorial team by email or telephone: dissonline@ub.fu-berlin.de Frau Meye 838-54276 and Frau Chue, 838-52708.

If your question is of a technical nature please visit "Tips and tricks"first, where you will likely find a solution if the problem has already arisen.

Advantages of depositing your Doctoral thesis or Habilitation treatise in the FU’s Institutional Repository

Depositing a copy of your dissertation in the institutional repository provides an option for publishing your work on an Open Access basis. The supplementary information you are required to provide (metadata) facilitates the retrieval of your work by search engines, and is used to generate the standard online title page for your work.

The dissertation is submitted as a PDF file or files, an electronic format that preserves a document’s layout for display and printing regardless of the system used to generate the document or the type of printer.

The pdf files must not have any security defaults (for example password protection). This is essential particularly with regard to data migration and/or long term archiving.

We recommend that you submit your doctoral thesis or habilitation treatise as a single pdf file if it is has a size of less than 50 MB. Should your work be bigger, we recommend that you divide it into several files to facilitate downloading.

Please keep in mind that your file(s) will be downloaded and that not all potential readers of your work will have highspeed Internet connections.

The file name is part of the hyperlink. Do not use umlauts, spaces, or special characters because many browsers in non-German speaking countries will not retrieve file names containing such characters. We reserve the right to reject any files with inappropriate names, and the author will be asked to provide a different name.

The UB will archive your dissertation on a permanent basis. To ensure long-term preservation and long-term accessibility the UB will convert or migrate formats should this become necessary. The printed and bound copies you are required to submit guarantee that your work also remains conventionally accessible.

Doctoral thesis or Habilitation treatise Format Requirements

If the original version of your dissertation contains colour illustrations, these should be retained in the electronic version. PDF files display images in colour and print to colour printers.

You will save yourself a lot of work if you use the style sheet function of your word processing program to format your dissertation. For example, do not simply mark and format headings in boldface or italics, but apply the appropriate style, such as Heading 1, Heading 2, and so on. Lists and tables should be generated with the appropriate tools, and not with tabs and spaces. Similarly, page breaks should be inserted using the appropriate command and not by inserting paragraph marks.

As mentioned above, avoid using special characters and formulas in the headings and abstracts of your dissertation. Headings and abstracts will be used in other connections where special characters cause a great deal of problems.

When documents are converted to PDF format this often causes changes in a document’s page layout. Thus we recommend that you use the PDF of your dissertation as the basis for printing the printed and bound copies that you are required to submit. Then you can be sure that the electronic and printed versions of your dissertation are the same. We accept black-and-white printouts of colour illustrations in the printed version of your dissertation.

Dissertationen online der Freien Universität Berlin


HaupttitelContributions to computing and modeling multiple whole-genome alignments
TitelvarianteBeiträge zur Berechnung und Modellierung multipler Alignments ganzer Genome
AutorKehr, Birte
Geburtsort: Braunschweig
GutachterProf. Dr. Knut Reinert
weitere GutachterProf. Aaron Darling, PhD
Freie SchlagwörterGenome alignment; sequene analysis; genome rearrangement
DDC570 Biowissenschaften; Biologie
004 Datenverarbeitung; Informatik
ZusammenfassungRecent advances in sequencing technologies have opened up the opportunity to study whole genomes at the nucleotide level. Similarities in the nucleotide sequences of genomes provide new insights in the relationships of organisms and species. Multiple whole-genome alignments represent these similarities, however their computation is challenging. In contrast to approaches for other sequence alignment problems, genome alignment methods have to deal with very long sequences and with non-colinearity of similarities.

This thesis makes three contributions to the development of multiple whole-genome alignment methods. The prevailing strategy of such methods is to combine a set of local alignments to a global genome alignment. This thesis suggests an efficient and fully sensitive local alignment approach, compares graph data structures for representing genome alignments, and describes hidden rearrangement breakpoints that become visible only in the comparison of more than two genomes.

All three contributions provide potential for significant improvements to the computation or modeling of genome alignments. In a comparison to other local alignment approaches, the new local aligner is the fastest of three fully sensitive ones and competitive with seed-and-extend approaches despite having full sensitivity. The assessment of graph data structures describes for the first time all graphs using the same terminology, and demonstrates how the graph structures differ in their information content. Finally, an analysis of breakpoints in simulated genome alignments suggests that hidden breakpoints are abundant and relevant for measuring the accuracy of genome alignments. In summary, the three contributions provide a promising basis for future genome alignment methods.
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SeitenzahlXVII, 161 S.
Fachbereich/EinrichtungFB Mathematik und Informatik
Rechte Nutzungsbedingungen
Tag der Disputation19.05.2014
Erstellt am11.06.2014 - 11:46:18
Letzte Änderung11.06.2014 - 11:50:13
Statische URLhttp://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000096799

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