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Parallelism In The SeqAn Library: 1D Load Balancing: Conceptual Draft Open issues * Providing N algorithm states to the forall method instead of just one intr…

template void remove(StringSet seq, StringSet qual, StringSet const adapter) { Align, ArrayGaps align; resize(rows(align), 2); for …

Page AdvancedAlgorithms This is the Wiki for a project oriented version of P4. Here you can find a StudentList Direct links to topics $ Algorithmic problems …

General information for programming exercises * Each group gets access to a svn directory at https://svn.mi.fu berlin.de/agbio/advancedAlgo/SS12/GroupX (Groups…

BScBlastInSeqAn A study comparing the classic NCBI BLAST implementation with a straightforward implementation in SeqAn. * Project Page Background BLAST 1 i…

Eine vergleichende Studie von BLAST Algorithmen Aufgabenstellung BLAST (Basic Local Alignment Tool) ist das bekannteste Programm zur Identifizierung von lokalen …

BScDataStructureSV SNP efficient Journal Strings Einleitung In den letzten 10 Jahren hat sich die Technologie zur Sequenzierung der DNS von Organismen kolossal v…

BScEfficientExactMotifDiscovery Implementation of an existing motif discovery algorithm in SeqAn. Background The goal of motif finding is the detection of novel…

BScGenAlignGraphs Comparing graphs for genome alignment of multiple sequences under the presence of large structural events. Schedule Moritz Finishing Date …

BScParallelBamIO Implementation of parallel de /compression of BAM files. * Parallel Bam I/O Schedule/Report Background BAM 1 files are used for storing ali…

BScParallelBamIOScheduleProject Implementation of parallel de /compression of BAM files Project Schedule Tasks 1) Extract the compression and decompression in…

BScReadRealignment Comparing short read realignment algorithms. Background Read alignment is a crucial step for the analysis of Next Generation Sequencing (NGS) …

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…

BscImprovementsOfGraphBasedRealignment Improving the Graph Based Realignment in SeqAn. Background The SeqAn library contains a powerful method for realignment an…

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 …

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…

BscRawSeqJournaling BSc Thesis: Journaling raw sequences. Weekly Progress Introduction Nowadays sequencing technologies lead to a tremendous number of available…

BscRegionFilter Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction "Many nucleotide and amino acid sequences are highly repetit…

Implementing 01*0 seed search strategy using the bidirectional FM index in SeqAn Background Approximate string matching is an important subtask in many bioinform…

BscSeqAnAlphabetReduction ((short description what this page is about)) introduction "Research on the functional redundancy of amino acids dates back t…

BscSeqAnAppInBrowser Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction Since modern web browsers are used for all kinds of tas…

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…

ChIP Seq Motivanalyse Konzept Bei der ChIP Seq Analyse werden die genomweiten Bindungsstellen von Transkriptionsfaktoren dadurch identifiziert, dass man die Tran…

Parallelism In The SeqAn Library: 1D Load Balancing With Divide Conquer: Conceptual Draft Related to 1DLoadBalancingConceptualDraft . This part looks at the …

Parallelism In The SeqAn Library: 1D Load Balancing: Conceptual Draft forall(AlgorithmState state, DataSpec spec) if spec is a leaf then process(state…

Extending SeqAn::TCoffe for deep alignments Area Mulitple Sequence Alignment Topic tbd. Timeline References 1. Rausch, T, Sergey Koren, Gennady Denisov, Da…

Page DfgWorkPackages This is the list of work packages from the DFG project. Design and verification of a suitable model for cross species genome compari son (...

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 …

Page Expose An expose for the Master's Thesis: "Journal Set: A container for utilizing Incremental Index Structures". Abstract In this Master's Thesis the concep…

Page FMIndex TITLE TITLE Student Jochen Singer Academic Advisor Prof. Dr. Knut Reinert, David Weese Expose Recent developments in the field of DN…

FM Index in Seqan

Flexbar Flexbar (flexible barcode and adapter removal) ist eine Software für das Postprocessing von Next Generation Sequencing Reads. Sie Umfasst die Funktionen …

Page GenomeComparisonP4 This is the project page of the Genome Comparison group. Students Mail an alle Gruppenmitglieder: AA2010SS GenComp bei lists.spline.de …

Page GenomicsLecture9Materials The script (lecture notes) for lectures 8/9 can be found on the wikipage for lecture 8. In that lecture, additional material about …

Timeline: * Week one: Preparation of the data (Matepairs, Illumina) for mapping, plus evaluation of the Matepair library quality. Choose suitable mapping program…

In diesem Praktikum geht es um die Erstellung von Software, um die Bindungsstellen von Transkriptionsfaktoren in DNA Sequenzen zu identifizieren und die Auswirkun…

Page JournalClubWS11 Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress reports fr…

Page JournalClubWS13 Welcome to the Wiki of the Journal Club (19576b) In this seminar we will present original work in Computational biology as well as progress r…

General info n this part of the Practical course sequence analysis you will be confronted with the situation of integrating several NGS analysis programs (which …

LaganHome Projektplanung und Umsetzung zur Implementierung von LAGAN Projektplan und Aufteilung 1. Start: Einlesen von FastA Dateien (Moritz) 2. Diese soll s…

LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntni…

OUT OF USE! Go to: https://kvv.imp.fu berlin.de/portal/ * SS 2018 * PMSB SeqAn * SS 2017 * PMSB SeqAn * SS 2016 * Journal Club * …

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…

Multi Split Mapping of NGS reads for variant detection Student Kathrin Trappe Academic Advisor Prof. Dr. Knut Reinert, Anne Katrin Emde Expose The goal …

MSc Thesis: Faster HMM Learning with Indexing Structures Motivation Hidden Markov Models (HMMs) are among the most prominent methods in Bioinformatics. They are …

PISB SeqAn Projekt Normalised Edit Distance Hintergrund: Normalisierte Edit Distanz Die Edit Distanz ist ein Standarddistanzmaß für Sequenzalignments, Mappings…

Projektmanagement im Softwarebereich Seqan 2010 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di…

Projektmanagement im Softwarebereich Seqan 2011 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di…

Projektmanagement im Softwarebereich SeqAn 2012 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Teilnehmer Name…

Projektmanagement im Softwarebereich SeqAn 2013 Dies ist die Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Alle Zeiten sind s.t. also w…

Projektmanagement im Softwarebereich, SoSe 2014 (19588a und 19588b) * Einführung in Software Engineering am Freitag entfällt leider! Dies ist die Wiki Seite z…

Projektmanagement im Softwarebereich, SoSe 2015 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" Se…

Projektmanagement im Softwarebereich, SoSe 2016 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" S…

Projektmanagement im Softwarebereich, SoSe 2017 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" S…

Projektmanagement im Softwarebereich, SoSe 2018 Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" SeqAn für BSc Studenten. Alle Z…

Page PSMB_Seqan_2013_BlastX Hintergrund: NGS Daten in Proteindatenbanken Next Generation Sequencing (NGS) Daten werden heute für unterschiedlichste Aufgaben verw…

Page PSMB_Seqan_2013_Lagan Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntniss…

NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver…

NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver…

Page PSMB_Seqan_2013_NGS_Quality_Control Hintegrund: NGS Quality Control Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichne…

PSMB_Seqan_2013_NGS_Quality_Control_Details_Features Our application will read fastq files and collect statistical data about its content. The input itself will n…

Page PSMB_Seqan_2013_PEMer PEMer overview, Figure 1 from (Korbel et al., 2009). Hintergrund: Paired End Signaturen und Strukturvarianten Als Strukturvarianten be…

Page PSMB_Seqan_2013_Suboptimal_Alignments Hintergrund: Suboptimale Alignments Lokale Alignments sind eine mächtige Methode um Sequenzhomologien zwischen zwei Se…

Schnelle Blastsuche durch Datenbank Clustering Hintergrund: Der Vergleich von Next Generation Sequencing (NGS) Daten gegen DNA oder Proteindatenbanken gehoert …

PSMB_Seqan_2014_SNP_caller Hintergrund Die häufigste und kleinste mögliche genomische Variation ist der Single Nucleotide Polymorphism. Nach dem Mapping von Read…

PSMB_Seqan_2014_large_insertd Hintergrund Lange Sequenzstücke, die im Donor aber nicht in der Referenz enthalten sind, lassen sich nur schwer mit einzelnen Reads…

PSMB_Seqan_2014_mapper Hintergrund Der erste Schritt ein einer Pipeline zur Analyse von Genomvarianten ist das Read Mapping. Dabei soll für jeden NGS Read eigent…

PSMB_Seqan_2014_overview Im PSMB SeqAn 2014 geht es darum, eine einfach Pipeline zur Variantenanalyse aufzubauen. Hintergrund Insbesondere für das menschliche Ge…

PSMB_Seqan_2014_small_indels Hintergrund Neben SNPs sind kleine Insertionen und Deletionen (indels) eine Klasse wichtiger genomischer Varianten. Für die Suche so…

Page PSMB_Seqan_2015_p2 Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse b…

PSMB_Seqan_2015_p3 Einleitung Eines der bekanntesten und meist genutzten Programme im Kontext der Bioinformatik ist NCBI Blast. Blast ist ein heuristisches Tool …

PSMB_Seqan_2015_p4 Introduction Trypsin is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. It cleaves peptide …

PSMB_Seqan_2015_p5 Introduction The q gram(k mer) Index in seqan allows looking up k mers over the index in constant time. However it has two limitations. The fi…

PSMB_Seqan_2015_palign Einleitung Paarweise Sequenzalignments liefern wertvolle biologische Informationen über die Identität zweier Sequenzen. Entsprechend w…

PSMB_Seqan_2016_p1 PMSB Project with possible Bachelor Project. Some experience with Javascript is required, some experience with C or C is recommended. Introdu…

Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Throug…

PSMB_Seqan_2016_p3 Hintergrund Der erste Schritt ein einer Pipeline zur Analyse von Genomvarianten ist das Read Mapping. Dabei soll für jeden NGS Read eigentlich…

PSMB_Seqan_2016_p4 In this project you will implement the typical Needleman Wunsch Algorithm, but with a few twists that will hopefully allow "auto vectorization"...

Add BAM support to SeqAn SequenceFile In this project you will be asked to write an interface that will help the Sequence IO of SeqAn to seamlessly read SAM/BAM f…

LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntni…

Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Throug…

PSMB_Seqan_2017_webassembly PMSB Project at the intersection of C , High performance computing and modern web technologies. Has the possibility to be continued as…

Auswertugn von Binning directories mit Hilfe von Interleaved Bloom filters Hintergrund: Filtern von NGS reads in bins In dem projekt soll (zufällig generierte) …

In this project a simple motif discovery algorithm should be implemented in SeqAn. Background The goal of motif finding is the detection of novel, unknown sign…

Detection of homologous regions with FFT Given a set of sequences your task is to compute homologous segments for all pairs of the input set. The detection of hom…

Parallel Suffix Array Construction Area Substring Indices Topic Das Suffix Array speichert die Anfänge aller Suffixe eines (oder mehrerer) Texte in lexikographi…

Page ProgressReportEmde 04 2010 Progress report Accomplishments in the last six months: General: * Read many papers on variant detection, notes taken here. …

Page ProgressReportEmde 05 2011 Progress Report (under construction) Accomplishments in the last six months: SplazerS: * redid single end read simulation (co…

Page ProgressReportEmde 10 2010 Progress Report Accomplishments in the last six months: Split read mapping: * Finished implementation of splitRazers, poster…

Page ProgressReportHu The purpose of this page is to make a schedule for my research progress and work plan for the next six months or more. Research progress a…

Page ProgressReportSiragusaFall2010 This is the progress report of Enrico Siragusa for the Fall 2010. Accomplishments up to the Fall 2010 * Familiarized with …

Praxismodule Applied Sequence Analysis Welcome to the Wiki of the Praxisseminar Applied Sequence Analysis News Times and rooms Rooms and timings Event …

// ================================================================ // quality_trimmer // ===================================...

AMS 3.0 predicting post translational modification sites Material Paper http://www.biomedcentral.com/1471 2105/11/210/abstract OpenMS docu: http://www bs2….

Area Computational RNA analysis Topic Extending structural RNA alignment algorithm to find regulatory motifs in mRNAs The project builds on work on structural…

Page Razers2Revision General Points TODO: Wait for evaluation of Hobbes on human, execute class, update tables. Manuel : Section S5 was updated to reflect the u…

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)...

reads.fastq This page contains the read.fastq file

Repeat Masking Repeats in DNA Sequenzen sind ein häufig beobachtetes Phänomen. Insbesondere in den ersten Schritten der Genome Analyse verursachen sie Probleme, d…

Research Cooperations The Reinert group at FU Berlin maintains research cooperations with German and international research groups. Note that this list here is no…

Meeting/Consultation minute 18 03 2014 Discussed Topics: * Genovo: Genovo is written in C . * Other metagenomic assemblers: Metavelvet, an extension of…

Research Logs * Genome Comparison (Birte Kehr, Manuel Holtgrewe) * Precursor Selection (Alexandra Zerck) * Indices and Applications (David Weese) * BW…

PISB SeqAn Projekt RNA Seq: Mapping von RNA reads mit MSplazer Hintergrund: Mapping von RNA reads Im Gegensatz zum Whole Genome Sequencing, wo ein kompletter…

Page RnaSeqP4 This is the project page of the RNA Seq group. Students Mail an alle Gruppenmitglieder: AA2010SS RNASeq bei lists.spline.de Name email Cori…

PISB SeqAn RNA Seq Read Simulator Hintergrund: RNA Seq Simulation Simulierte Daten leisten wichtige Dienste bei der Entwicklung, Fehlersuche und Bewertung von …

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 …

Implementation and evaluation of index based seeding strategies in SeqAn Area Substring Indices, read mapping, local alignment, q mer indices Topic The goal of …

PISB SeqAn Teilprojekte Segment Aligner Hintergrund: Hierarchisches Genomalignment Um das Alignment ganzer Genome zu ermöglichen, werden in der Regel zunächst …

Information about the SeqAn retreat Please keep checking for updates! Schedule The meeting begins on Monday, 04 Oct 2010 at 10 a.m. and ends on Friday, 08 Oct 20…

Information about the SeqAn workshop 2011 The SeqAn BioStore website is up. Please find information here.

Guidelines for the Organization of Meetings Technical Factors * find/reserve a room SeqAn Retreat March 2012 with Illumina: T9/053 * look into technical…

Sequence Analysis, SoSe 2014 (LV Nr. 19716, 19716a, 19716b) Welcome to the Wiki of Sequence Analysis. This module consists of 2 hours lecture, 2 hours exercis…

Sequence Analysis, SoSe 2015 (LV Nr. 19401601 (V), 19401602 (Ü), 19401611 (S)) Welcome to the Wiki of Sequence Analysis. This module consists of 2 hours lectu…

Sequence Analysis, SoSe 2016 *(LV Nr. 19401601 (V), 19401602 (Ü), 19401611 (S)) Welcome to the Wiki of Sequence Analysis. Dear Students. We will use for the lec…

Simple Bowtie Bowtie ist ein "ultrafast and memory efficient" Read Mapper 1 der auf der Burrows Wheeler Transformation (BWT) basiert. Die BWT eines Textes T ist…

SLAGAN Input: two genomic dna sequences in FASTA file(s) Generation of local alignments (Svenja) SLAGAN uses the CHAOS aligner for this phase: * finding seeds…

Page SnippetsAnneKatrin This is where I write my weekly goals. all time todos: * make splitRazers project page * add link in seqanswers forum srp thread …

SpaceEfficientBWTConstruction Implementation of a fast and memory efficient BWT construction algorithm. Background The Burrows Wheehler Transform transforms a te…

Write a SeqAn program that: * reads in….

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…

Page StellarMotifFinderWeeklyReports These are brief weekly reports about the status of the BSc Thesis StellarMotifFinder. Week 1 (25.07.2012 31.07.2012) * …

Page StellarTuning export CPUPROFILE=stellar.prof LD_PRELOAD="/usr/lib/libprofiler.so.0" ./stellar d hs_ref_chr10.fa q contig_0000aa.fa.2000 l 30 k 16 e 0.03…

StundenPlan Reinert / Piro / Marsico SoSe 2017 time: Monday Tuesday Wednesday Thursday Friday 8 10 10 12 SeqAnalys (VL) 051/t9 …

Theses Page OUTDATED! Go to: https://kvv.imp.fu berlin.de/x/8RK4cp Available topics * If you are interested in doing your thesis in algorithmic bioinformatic…

Approximate String Matching (Hamming Distance) This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn…

Page ThesisCNVs Detektion von Copy Number Variationen in Sequenzierdaten $ Student: Kerstin Neubert $ Betreuer: Anne Katrin Emde, Prof. Dr. Knut Reinert Z…

Page ThesisGPGPUSeqan Myers Bit Vector Algorithm on GPU for Seqan Massiv parallelization of Myers Fast Bit Vector Algorithm for Approximate String Matchinsg us…

ThesisMCRazer Check, whether abstract, description, and literature are in CMS Parallelization of RazerS $ Student: Martin Riese $ Academic Advisor: David W…

Page ThesisMeganRazersReports Weekly Reports for the Bachelor Thesis "Comparative Genomics with MEGAN and RazerS" by Hannes Hauswedell Week 1 (2009 07 11..2009 0…

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…

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…

Complemented palindromes Zusammenfassung Implementierung und Vergleich drei verschiedener Ansätze zum Finden von maximalen, komplementären Palindromen einer sign…

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…

Parallelism In The SeqAn Library: Patterns for Parallelization A brief summary of patterns for parallelization, based on Massingill et al. 2000 . Finding Concur…

Parallelism In The SeqAn Library: #8220;Weekly #8221; Reports Weekly reports about ThesisParallelismInSeqan. General * 05/08 #8211;05/11: * Work on pre…

Parallelism In The SeqAn Library: Schedule Tentative Schedule Tentative total: 25 weeks. Review of existing literature and other implementations (2 #8211;4 weeks…

Scaling genome alignment to hundreds of genomes Topic With the rapid development of next generation sequencing technologies more and more genomes are being seque…

Substitution Matrix Generation Algorithms This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn, sou…

BLAST Implementation in SeqAn Es soll ein BLASTX (Nukleotidsequenz 6 fach translatieren und gegen Proteindatenbank abgleichen) 'from scratch' für die SeqAn Bib…

The data for this project comes from the company febit. The goal is to: 1. Develop a local read mapper for color spaced reads. 2. To apply it to find viral …

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…

Statistics for ABI Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: …

Weekly Report for the DFG project: Algorithm Engineering for High Throughput Sequencing Data Summarizes the weekly progress of the DFG project. Jul 2011 * 01….

Page Worklog_Hauswedell Project Work log Hauswedell Friday, 25.06.2010: * second "real" meeting with Thieme to do planning and division of work * got access…

Wartung Fachbereich Mathematik und InformatikIT Dienst Wartungsplanung bzw. status für die IT Wartung am Mittwoch, 5. August 2020 Details und Zeitplan zu den …

ol li { margin top: 14px; margin bottom: 14px; } Publications of the Software Engineering Research Group See ResearchHome for a description of the researc…

Research of AG SE The Software Engineering research group is concerned with reducing the gap between the State of the Art and the average State of the Practice in…