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BScBlastInSeqAn
BScBlastInSeqAn A study comparing the classic NCBI BLAST implementation with a straightforward implementation in SeqAn. * Project Page Background BLAST 1 i...
r3 - 25 Jun 2013 - 13:26 by annkatrin
BScDataStructureSV
BScDataStructureSV SNP efficient Journal Strings Einleitung In den letzten 10 Jahren hat sich die Technologie zur Sequenzierung der DNS von Organismen kolossal v...
NEW - 25 Nov 2013 - 22:38 by RmaerkerUserTopic
BScEfficientExactMotifDiscovery
BScEfficientExactMotifDiscovery Implementation of an existing motif discovery algorithm in SeqAn. Background The goal of motif finding is the detection of novel...
NEW - 06 Jun 2013 - 14:02 by holtgrew
BScGenAlignGraphs
BScGenAlignGraphs Comparing graphs for genome alignment of multiple sequences under the presence of large structural events. Schedule Moritz Finishing Date ...
r9 - 19 Sep 2013 - 15:22 by kiekemo
BScParallelBamIO
BScParallelBamIO Implementation of parallel de /compression of BAM files. * Parallel Bam I/O Schedule/Report Background BAM 1 files are used for storing ali...
r5 - 21 Oct 2013 - 11:08 by holtgrew
BScReadRealignment
BScReadRealignment Comparing short read realignment algorithms. Background Read alignment is a crucial step for the analysis of Next Generation Sequencing (NGS) ...
NEW - 30 May 2013 - 22:53 by holtgrew
BiBWTApps
MSc Thesis The birectional BWT and its applications Topic TODO Journal * 2014 09 15: I read up on templates, forked the official seqan repository, set Ecli...
r18 - 15 Nov 2014 - 17:00 by cpockrandt
BlastX
BlastX Diese Seite stellt das Wiki zur BlastX Implementierung von Hannes Hauswedel dar. Zusammenfassung BLASTX ist ein Programm zum Finden von Nucleotid Sequenze...
NEW - 25 Mar 2013 - 15:05 by jsinger
BscImprovementsOfGraphBasedRealignment
BscImprovementsOfGraphBasedRealignment Improving the Graph Based Realignment in SeqAn. Background The SeqAn library contains a powerful method for realignment an...
r3 - 20 Jun 2013 - 10:19 by holtgrew
BscKmerBinCounting
Implementing and evaluating different strategies to assign the set of k mers in a NGS sample to genomic bins Background For metagenomics read mapping it becomes ...
NEW - 29 Nov 2017 - 12:01 by ReinertUserTopic
BscPlagiarismApp
Implementation of an IOS app to compare documents and visualize common paragraphs using a local alignment software. Background The goal of this thesis is to adap...
r2 - 19 Sep 2014 - 10:01 by ReinertUserTopic
BscRawSeqJournaling
BscRawSeqJournaling BSc Thesis: Journaling raw sequences. Weekly Progress Introduction Nowadays sequencing technologies lead to a tremendous number of available...
r3 - 12 Feb 2015 - 19:05 by RmaerkerUserTopic
BscRegionFilter
BscRegionFilter Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction "Many nucleotide and amino acid sequences are highly repetit...
r3 - 24 Oct 2017 - 15:59 by h4nn3s
BscSeqAnAlphabetReduction
BscSeqAnAlphabetReduction ((short description what this page is about)) introduction "Research on the functional redundancy of amino acids dates back t...
NEW - 09 Mar 2017 - 15:59 by h4nn3s
BscSeqAnAppInBrowser
BscSeqAnAppInBrowser Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction Since modern web browsers are used for all kinds of tas...
NEW - 06 Oct 2015 - 18:53 by h4nn3s
BscSeqAnOpenMSPeptideIndexer
Peptide Indexer using SeqAn and OpenMS Background In Proteomics one subtask for Peptide ID is to search peptide sequences in protein databases. This thesis shall...
NEW - 22 Mar 2016 - 22:10 by ReinertUserTopic
BscTreeBasedMapAlignment
BscTreeBasedMapAlignment B.Sc. topic proposal in high throughput proteomics Focus * Programming: ** * Math: ** * Biology: * Introduction LC MS data i...
NEW - 25 Apr 2017 - 17:09 by BielowUserTopic
CaptureCompoundMS
Devising read mapping strategies in KNIME Area Proteomics, label free quantitation, data bases Topic tbd. Timeline tbd References tbd.
NEW - 03 May 2013 - 10:29 by ReinertUserTopic
ChipSeqAnalysis
MSc Thesis #8211; Analysis of protein DNA interactions from ChIP seq data Remark This thesis will be a joint project of the Algorithmische Bioinformatik group a...
NEW - 06 Nov 2012 - 22:15 by SandroAndreotti
ChipSeqProfiles
Übersicht ChIP Seq ist eine Methode zur genomweiten Untersuchung von Protein DNA Interaktion 1 . Mit Hilfe von Antikörpern werden die Proteine von Interesse geme...
NEW - 20 Jun 2011 - 18:30 by KnutReinert
DeepCoffee
Extending SeqAn::TCoffe for deep alignments Area Mulitple Sequence Alignment Topic tbd. Timeline References 1. Rausch, T, Sergey Koren, Gennady Denisov, Da...
NEW - 02 Oct 2014 - 22:09 by ReinertUserTopic
EclipsePluging
BSc Thesis: Developing an Eclipse plugin for SeqAn Motivation SeqAn is an open source C library of efficient algorithms and data structures for the analysis of ...
r2 - 25 Oct 2011 - 21:00 by BjoernKahlert
FMIndex
Page FMIndex TITLE TITLE Student Jochen Singer Academic Advisor Prof. Dr. Knut Reinert, David Weese Expose Recent developments in the field of DN...
r11 - 27 Jun 2011 - 13:46 by JochenSinger
FMTree
Improving Location Algorithms in FM indices Implementation of FMtrees A recently published paper improves the location time (retrieving positions in the text) f...
NEW - 30 May 2018 - 16:40 by cpockrandt
Flexbar
Flexbar Flexbar (flexible barcode and adapter removal) ist eine Software für das Postprocessing von Next Generation Sequencing Reads. Sie Umfasst die Funktionen ...
r13 - 16 Sep 2013 - 14:43 by serosko
GenomeEvolutionSimulator
MSc Thesis: Simulation of Genomes and Genome Evolution Also see the attached PDF file with figures. Motivation The explosion of the availability of genomic data ...
r2 - 29 Jun 2011 - 15:44 by ManuelHoltgrewe
GuineaPigAnnotation
Timeline: * Week one: Preparation of the data (Matepairs, Illumina) for mapping, plus evaluation of the Matepair library quality. Choose suitable mapping program...
r2 - 23 Mar 2012 - 10:28 by KnutReinert
LastImplementation
Implementation of LAST with gapped seeds and applications to read mapping and local alignment Area Substring Indices, read mapping, local alignment Topic The go...
r3 - 30 Apr 2013 - 09:39 by ReinertUserTopic
MethylationMapping
Multi Split Mapping of NGS reads for variant detection Student Sabrina Krakau Academic Advisor Prof. Dr. Knut Reinert, Anne Katrin Emde Expose The goal ...
r4 - 21 Feb 2012 - 13:50 by SabrinaKrakau
MultiReadAssignment
Solving the Multi read assignment problem Description This thesis should provide new ideas to solve the problem of multi read assignment for NGS data. Based on...
r7 - 06 Jul 2011 - 14:16 by lkuchenb
MultiSplitMappingNGS
Multi Split Mapping of NGS reads for variant detection Student Kathrin Trappe Academic Advisor Prof. Dr. Knut Reinert, Anne Katrin Emde Expose The goal ...
r14 - 02 May 2013 - 12:21 by KtrappeUserTopic
NewHMMLearningAlgorithms
MSc Thesis: Faster HMM Learning with Indexing Structures Motivation Hidden Markov Models (HMMs) are among the most prominent methods in Bioinformatics. They are ...
NEW - 14 Sep 2011 - 11:32 by KnutReinert
ParallelSuffixArray
Parallel Suffix Array Construction Area Substring Indices Topic Das Suffix Array speichert die Anfänge aller Suffixe eines (oder mehrerer) Texte in lexikographi...
NEW - 31 Oct 2012 - 09:58 by DavidWeese
RNAAligner
Area Computational RNA analysis Topic Extending structural RNA alignment algorithm to find regulatory motifs in mRNAs The project builds on work on structural...
r2 - 10 Feb 2012 - 09:50 by KnutReinert
ReadMapper
Devising read mapping strategies in KNIME Area Read mapping quality, Mappability, KNIME Topic The main goal of this thesis is to devise strategies to compute a)...
r5 - 26 Aug 2013 - 12:07 by kys
SIMDDpAlgo
SIMDDpAlgo SIMD extension of the standard DP algorithms in SeqAn Introduction Newer processors are shipped with 16 registers having an extended width of 128 bit ...
r2 - 12 Mar 2015 - 23:08 by RmaerkerUserTopic
SeedingStrategies
Implementation and evaluation of index based seeding strategies in SeqAn Area Substring Indices, read mapping, local alignment, q mer indices Topic The goal of ...
r2 - 27 Jan 2016 - 14:58 by ReinertUserTopic
SpaceEfficientBWTConstruction
SpaceEfficientBWTConstruction Implementation of a fast and memory efficient BWT construction algorithm. Background The Burrows Wheehler Transform transforms a te...
r7 - 11 Jul 2013 - 16:19 by zer
StellarMotifFinder
Topic Motif finding using the STELLAR engine and SeqAn::TCoffee The project builds on work on exact local alignment by Kehr, Rausch, Emde and Reinert 1,2 . STEL...
r3 - 25 Jul 2012 - 11:09 by BirteKehr
SuffixArrayConstruction
Implementation of Suffix Array Construction Algorithms The SDSL (Succinct Data Structure Library) has various implementations of string indices based on suffix ar...
NEW - 30 May 2018 - 16:19 by cpockrandt
ThesisAnnoAlign
Page ThesisAnnoAlign Brief overview Next generation sequencing methods have given rise to a whole new set of algorithmic problems. Using the principles of huge a...
r3 - 16 Nov 2009 - 18:06 by mheuser
ThesisApproxHammingMatch
Approximate String Matching (Hamming Distance) This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn...
r4 - 02 Jan 2011 - 22:05 by ManuelHoltgrewe
ThesisBScMyriMatch
Implementation and Evaluation of a Myrimatch Adapter Student Dimitri Schachmann Academic Advisor Prof. Dr. Knut Reinert, Chris Bielow Expose The goal of...
r5 - 20 Apr 2012 - 14:58 by SchachmaUserTopic
ThesisCNVs
Page ThesisCNVs Detektion von Copy Number Variationen in Sequenzierdaten $ Student: Kerstin Neubert $ Betreuer: Anne Katrin Emde, Prof. Dr. Knut Reinert Z...
r20 - 30 Jul 2010 - 00:35 by NeubertkUserTopic
ThesisGPGPUSeqan
Page ThesisGPGPUSeqan Myers Bit Vector Algorithm on GPU for Seqan Massiv parallelization of Myers Fast Bit Vector Algorithm for Approximate String Matchinsg us...
r28 - 22 Mar 2011 - 22:35 by llangner
ThesisGenomesPerMail
Page ThesisGenomesPerMail ((short description what this page is about)) Expose Rene, please write an expose for the thesis here with the following tasks. Task...
r7 - 27 May 2010 - 16:20 by RmaerkerUserTopic
ThesisIncrementalIndices
Page ThesisIncrementalIndices ((short description what this page is about)) Currently working On Performance tests and improvement of Journal String Class Secti...
NEW - 30 Sep 2009 - 14:47 by PylUserTopic
ThesisMCRazer
ThesisMCRazer Check, whether abstract, description, and literature are in CMS Parallelization of RazerS $ Student: Martin Riese $ Academic Advisor: David W...
r4 - 03 Feb 2010 - 09:03 by mriese
ThesisMeganRazers
Page ThesisMeganRazers brief overview * continue/finish implementation of RazerBlastS, an adaptation of RazerS, aimed at providing BLAST like options and comp...
r3 - 15 Sep 2009 - 15:28 by hauswede
ThesisNGSOverlap
Overlap Module for NGS Pipeline Summary The overlap module merges the information retained by read mapping to a genome with annotation information (for example g...
r4 - 16 Aug 2009 - 21:30 by krakau
ThesisNgsCleaning
NGS Data Cleaning TODO: Manuel Note that we can shift the focus of the thesis much stronger towards programming/implementation if you want to program! Next Genera...
r4 - 15 Jun 2012 - 11:00 by KnutReinert
ThesisPalindromes
Complemented palindromes Zusammenfassung Implementierung und Vergleich drei verschiedener Ansätze zum Finden von maximalen, komplementären Palindromen einer sign...
r3 - 10 Sep 2009 - 11:40 by fheeger
ThesisParallelismInSeqan
Parallelism In The SeqAn Library The purpose of this thesis is to allow "easy parallelism" in the SeqAn library. This will consist of identifying parts of the lib...
r5 - 10 Sep 2010 - 14:50 by ManuelHoltgrewe
ThesisProposals
Thesis Proposals OUTDATED! Go to: https://kvv.imp.fu berlin.de/x/8RK4cp Here is the section for BSc and MSc students. At the beginning of the thesis the student ...
r3 - 23 Sep 2019 - 11:21 by KasseckeUserTopic
r7 - 01 Mar 2011 - 13:38 by phansen
ThesisSCFGs
Page ThesisSCFGs ((short description what this page is about)) (1) The software part and what has been done so far: parsing of scfg data from files transforma...
NEW - 19 Jan 2010 - 16:52 by KnutReinert
ThesisScalingGenomeAlignment
Scaling genome alignment to hundreds of genomes Topic With the rapid development of next generation sequencing technologies more and more genomes are being seque...
NEW - 19 Mar 2012 - 11:23 by BirteKehr
ThesisScoreMatrix
Substitution Matrix Generation Algorithms This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn, sou...
r2 - 08 Apr 2010 - 14:25 by KnutReinert
ThesisSeqAnBlast
BLAST Implementation in SeqAn Es soll ein BLASTX (Nukleotidsequenz 6 fach translatieren und gegen Proteindatenbank abgleichen) 'from scratch' für die SeqAn Bib...
r12 - 15 Sep 2012 - 10:31 by fsiemer
WebPreferences
ABI Web Preferences The following settings are web preferences of the ABI web. These preferences overwrite the site level preferences in . and , and can b...
r26 - 07 Mar 2014 - 21:01 by weese
WebStatistics
Statistics for ABI Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: ...
r609 - 13 May 2025 - 04:03 by AdminUser
WholeTranscriptomeAnalysis
MSc Thesis Whole transcriptome and miRNome analysis from next generation sequencing data Remark This thesis will be a joint project of the Algorithmische Bioin...
NEW - 06 Nov 2012 - 22:09 by SandroAndreotti
Number of topics: 62
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