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1DLoadBalancingConceptualDraft
in ABI
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…
AdapterRemoval
in ABI
template void remove(StringSet seq, StringSet qual, StringSet const adapter) { Align, ArrayGaps align; resize(rows(align), 2); for …
AdvancedAlgorithms
in ABI
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 …
AssignmentWeek1
in ABI
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
in ABI
BScBlastInSeqAn A study comparing the classic NCBI BLAST implementation with a straightforward implementation in SeqAn. * Project Page Background BLAST 1 i…
BScBlastInSeqAnProject
in ABI
Eine vergleichende Studie von BLAST Algorithmen Aufgabenstellung BLAST (Basic Local Alignment Tool) ist das bekannteste Programm zur Identifizierung von lokalen …
BScDataStructureSV
in ABI
BScDataStructureSV SNP efficient Journal Strings Einleitung In den letzten 10 Jahren hat sich die Technologie zur Sequenzierung der DNS von Organismen kolossal v…
BScEfficientExactMotifDiscovery
in ABI
BScEfficientExactMotifDiscovery Implementation of an existing motif discovery algorithm in SeqAn. Background The goal of motif finding is the detection of novel…
BScGenAlignGraphs
in ABI
BScGenAlignGraphs Comparing graphs for genome alignment of multiple sequences under the presence of large structural events. Schedule Moritz Finishing Date …
BScParallelBamIO
in ABI
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
in ABI
BScParallelBamIOScheduleProject Implementation of parallel de /compression of BAM files Project Schedule Tasks 1) Extract the compression and decompression in…
BScReadRealignment
in ABI
BScReadRealignment Comparing short read realignment algorithms. Background Read alignment is a crucial step for the analysis of Next Generation Sequencing (NGS) …
BiBWTApps
in ABI
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
in ABI
BscImprovementsOfGraphBasedRealignment Improving the Graph Based Realignment in SeqAn. Background The SeqAn library contains a powerful method for realignment an…
BscKmerBinCounting
in ABI
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 …
BscPlagiarismApp
in ABI
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
in ABI
BscRawSeqJournaling BSc Thesis: Journaling raw sequences. Weekly Progress Introduction Nowadays sequencing technologies lead to a tremendous number of available…
BscRegionFilter
in ABI
BscRegionFilter Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction "Many nucleotide and amino acid sequences are highly repetit…
BscSeqAn010Seeds
in ABI
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
in ABI
BscSeqAnAlphabetReduction ((short description what this page is about)) introduction "Research on the functional redundancy of amino acids dates back t…
BscSeqAnAppInBrowser
in ABI
BscSeqAnAppInBrowser Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction Since modern web browsers are used for all kinds of tas…
BscSeqAnOpenMSPeptideIndexer
in ABI
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…
ChipSeq
in ABI
ChIP Seq Motivanalyse Konzept Bei der ChIP Seq Analyse werden die genomweiten Bindungsstellen von Transkriptionsfaktoren dadurch identifiziert, dass man die Tran…
DCLoadBalancingConceptualDraft
in ABI
Parallelism In The SeqAn Library: 1D Load Balancing With Divide Conquer: Conceptual Draft Related to 1DLoadBalancingConceptualDraft . This part looks at the …
DCStaticLoadBalancing
in ABI
Parallelism In The SeqAn Library: 1D Load Balancing: Conceptual Draft forall(AlgorithmState state, DataSpec spec) if spec is a leaf then process(state…
DeepCoffee
in ABI
Extending SeqAn::TCoffe for deep alignments Area Mulitple Sequence Alignment Topic tbd. Timeline References 1. Rausch, T, Sergey Koren, Gennady Denisov, Da…
DfgWorkPackages
in ABI
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 (...
EclipsePluging
in ABI
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 …
Expose
in ABI
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…
FMIndex
in ABI
Page FMIndex TITLE TITLE Student Jochen Singer Academic Advisor Prof. Dr. Knut Reinert, David Weese Expose Recent developments in the field of DN…
Flexbar
in ABI
Flexbar Flexbar (flexible barcode and adapter removal) ist eine Software für das Postprocessing von Next Generation Sequencing Reads. Sie Umfasst die Funktionen …
GenomeComparisonP4
in ABI
Page GenomeComparisonP4 This is the project page of the Genome Comparison group. Students Mail an alle Gruppenmitglieder: AA2010SS GenComp bei lists.spline.de …
GenomicsLecture9Materials
in ABI
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 …
GuineaPigAnnotation
in ABI
Timeline: * Week one: Preparation of the data (Matepairs, Illumina) for mapping, plus evaluation of the Matepair library quality. Choose suitable mapping program…
JMatch
in ABI
In diesem Praktikum geht es um die Erstellung von Software, um die Bindungsstellen von Transkriptionsfaktoren in DNA Sequenzen zu identifizieren und die Auswirkun…
JournalClubWS11
in ABI
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…
JournalClubWS13
in ABI
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…
KnimeSec
in ABI
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
in ABI
LaganHome Projektplanung und Umsetzung zur Implementierung von LAGAN Projektplan und Aufteilung 1. Start: Einlesen von FastA Dateien (Moritz) 2. Diese soll s…
LaganSeqan2018
in ABI
LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntni…
LectureWiki
in ABI
OUT OF USE! Go to: https://kvv.imp.fu berlin.de/portal/ * SS 2018 * PMSB SeqAn * SS 2017 * PMSB SeqAn * SS 2016 * Journal Club * …
MultiReadAssignment
in ABI
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…
MultiSplitMappingNGS
in ABI
Multi Split Mapping of NGS reads for variant detection Student Kathrin Trappe Academic Advisor Prof. Dr. Knut Reinert, Anne Katrin Emde Expose The goal …
NewHMMLearningAlgorithms
in ABI
MSc Thesis: Faster HMM Learning with Indexing Structures Motivation Hidden Markov Models (HMMs) are among the most prominent methods in Bioinformatics. They are …
NormEditDist
in ABI
PISB SeqAn Projekt Normalised Edit Distance Hintergrund: Normalisierte Edit Distanz Die Edit Distanz ist ein Standarddistanzmaß für Sequenzalignments, Mappings…
PMSB_Seqan_2010
in ABI
Projektmanagement im Softwarebereich Seqan 2010 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di…
PMSB_Seqan_2011
in ABI
Projektmanagement im Softwarebereich Seqan 2011 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di…
PMSB_Seqan_2012
in ABI
Projektmanagement im Softwarebereich SeqAn 2012 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Teilnehmer Name…
PMSB_Seqan_2013
in ABI
Projektmanagement im Softwarebereich SeqAn 2013 Dies ist die Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Alle Zeiten sind s.t. also w…
PMSB_Seqan_2014
in ABI
Projektmanagement im Softwarebereich, SoSe 2014 (19588a und 19588b) * Einführung in Software Engineering am Freitag entfällt leider! Dies ist die Wiki Seite z…
PMSB_Seqan_2015
in ABI
Projektmanagement im Softwarebereich, SoSe 2015 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" Se…
PMSB_Seqan_2016
in ABI
Projektmanagement im Softwarebereich, SoSe 2016 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" S…
PMSB_Seqan_2017
in ABI
Projektmanagement im Softwarebereich, SoSe 2017 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" S…
PMSB_Seqan_2018
in ABI
Projektmanagement im Softwarebereich, SoSe 2018 Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" SeqAn für BSc Studenten. Alle Z…
PSMB_Seqan_2013_BlastX
in ABI
Page PSMB_Seqan_2013_BlastX Hintergrund: NGS Daten in Proteindatenbanken Next Generation Sequencing (NGS) Daten werden heute für unterschiedlichste Aufgaben verw…
PSMB_Seqan_2013_Lagan
in ABI
Page PSMB_Seqan_2013_Lagan Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntniss…
PSMB_Seqan_2013_NGS_Data_Cleansing
in ABI
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver…
PSMB_Seqan_2013_NGS_Data_Cleansing_New
in ABI
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver…
PSMB_Seqan_2013_NGS_Quality_Control
in ABI
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_PEMer
in ABI
Page PSMB_Seqan_2013_PEMer PEMer overview, Figure 1 from (Korbel et al., 2009). Hintergrund: Paired End Signaturen und Strukturvarianten Als Strukturvarianten be…
PSMB_Seqan_2013_Suboptimal_Alignments
in ABI
Page PSMB_Seqan_2013_Suboptimal_Alignments Hintergrund: Suboptimale Alignments Lokale Alignments sind eine mächtige Methode um Sequenzhomologien zwischen zwei Se…
PSMB_Seqan_2013_UBlast
in ABI
Schnelle Blastsuche durch Datenbank Clustering Hintergrund: Der Vergleich von Next Generation Sequencing (NGS) Daten gegen DNA oder Proteindatenbanken gehoert …
PSMB_Seqan_2014_SNP_caller
in ABI
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
in ABI
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
in ABI
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
in ABI
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
in ABI
PSMB_Seqan_2014_small_indels Hintergrund Neben SNPs sind kleine Insertionen und Deletionen (indels) eine Klasse wichtiger genomischer Varianten. Für die Suche so…
PSMB_Seqan_2015_p2
in ABI
Page PSMB_Seqan_2015_p2 Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse b…
PSMB_Seqan_2015_p3
in ABI
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
in ABI
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
in ABI
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
in ABI
PSMB_Seqan_2015_palign Einleitung Paarweise Sequenzalignments liefern wertvolle biologische Informationen über die Identität zweier Sequenzen. Entsprechend w…
PSMB_Seqan_2016_p1
in ABI
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…
PSMB_Seqan_2016_p2
in ABI
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
in ABI
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 ABI
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"...
PSMB_Seqan_2016_p5
in ABI
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…
PSMB_Seqan_2016_p6
in ABI
LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntni…
PSMB_Seqan_2017_p1
in ABI
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
in ABI
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…
PSMB_Seqan_IBF
in ABI
Auswertugn von Binning directories mit Hilfe von Interleaved Bloom filters Hintergrund: Filtern von NGS reads in bins In dem projekt soll (zufällig generierte) …
PSMB_Seqan_MF
in ABI
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…
PSMB_Seqan_fft
in ABI
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…
ParallelSuffixArray
in ABI
Parallel Suffix Array Construction Area Substring Indices Topic Das Suffix Array speichert die Anfänge aller Suffixe eines (oder mehrerer) Texte in lexikographi…
ProgressReportEmde-04-2010
in ABI
Page ProgressReportEmde 04 2010 Progress report Accomplishments in the last six months: General: * Read many papers on variant detection, notes taken here. …
ProgressReportEmde-05-2011
in ABI
Page ProgressReportEmde 05 2011 Progress Report (under construction) Accomplishments in the last six months: SplazerS: * redid single end read simulation (co…
ProgressReportEmde-10-2010
in ABI
Page ProgressReportEmde 10 2010 Progress Report Accomplishments in the last six months: Split read mapping: * Finished implementation of splitRazers, poster…
ProgressReportHu
in ABI
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…
ProgressReportSiragusaFall2010
in ABI
Page ProgressReportSiragusaFall2010 This is the progress report of Enrico Siragusa for the Fall 2010. Accomplishments up to the Fall 2010 * Familiarized with …
QualityTrim
in ABI
// ================================================================
// quality_trimmer // ===================================
...
QuantProtP4_AMS
in ABI
AMS 3.0 predicting post translational modification sites Material Paper http://www.biomedcentral.com/1471 2105/11/210/abstract OpenMS docu: http://www bs2….
RNAAligner
in ABI
Area Computational RNA analysis Topic Extending structural RNA alignment algorithm to find regulatory motifs in mRNAs The project builds on work on structural…
Razers2Revision
in ABI
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…
ReadMapper
in ABI
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
in ABI
reads.fastq This page contains the read.fastq file
RepeatMasking
in ABI
Repeat Masking Repeats in DNA Sequenzen sind ein häufig beobachtetes Phänomen. Insbesondere in den ersten Schritten der Genome Analyse verursachen sie Probleme, d…
ResearchCooperations
in ABI
Research Cooperations The Reinert group at FU Berlin maintains research cooperations with German and international research groups. Note that this list here is no…
ResearchLogTemesgenDadi18032014
in ABI
Meeting/Consultation minute 18 03 2014 Discussed Topics: * Genovo: Genovo is written in C . * Other metagenomic assemblers: Metavelvet, an extension of…
ResearchLogs
in ABI
Research Logs * Genome Comparison (Birte Kehr, Manuel Holtgrewe) * Precursor Selection (Alexandra Zerck) * Indices and Applications (David Weese) * BW…
RnaSeqMSplazers
in ABI
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…
RnaSeqP4
in ABI
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…
RnaSeqReadSimulator
in ABI
PISB SeqAn RNA Seq Read Simulator Hintergrund: RNA Seq Simulation Simulierte Daten leisten wichtige Dienste bei der Entwicklung, Fehlersuche und Bewertung von …
SIMDDpAlgo
in ABI
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 …
SeedingStrategies
in ABI
Implementation and evaluation of index based seeding strategies in SeqAn Area Substring Indices, read mapping, local alignment, q mer indices Topic The goal of …
SegementAligner
in ABI
PISB SeqAn Teilprojekte Segment Aligner Hintergrund: Hierarchisches Genomalignment Um das Alignment ganzer Genome zu ermöglichen, werden in der Regel zunächst …
SeqAnRetreat2010
in ABI
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…
SeqAnRetreat2011
in ABI
Information about the SeqAn workshop 2011 The SeqAn BioStore website is up. Please find information here.
SeqAnRetreat2012
in ABI
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_2014
in ABI
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_2015
in ABI
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_2016
in ABI
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…
SimpleBowtie
in ABI
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…
SlaganSupermap
in ABI
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…
SnippetsAnneKatrin
in ABI
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
in ABI
SpaceEfficientBWTConstruction Implementation of a fast and memory efficient BWT construction algorithm. Background The Burrows Wheehler Transform transforms a te…
StellarMotifFinder
in ABI
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…
StellarMotifFinderWeeklyReports
in ABI
Page StellarMotifFinderWeeklyReports These are brief weekly reports about the status of the BSc Thesis StellarMotifFinder. Week 1 (25.07.2012 31.07.2012) * …
StellarTuning
in ABI
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
in ABI
StundenPlan Reinert / Piro / Marsico SoSe 2017 time: Monday Tuesday Wednesday Thursday Friday 8 10 10 12 SeqAnalys (VL) 051/t9 …
ThesesHome
in ABI
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…
ThesisApproxHammingMatch
in ABI
Approximate String Matching (Hamming Distance) This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn…
ThesisCNVs
in ABI
Page ThesisCNVs Detektion von Copy Number Variationen in Sequenzierdaten $ Student: Kerstin Neubert $ Betreuer: Anne Katrin Emde, Prof. Dr. Knut Reinert Z…
ThesisGPGPUSeqan
in ABI
Page ThesisGPGPUSeqan Myers Bit Vector Algorithm on GPU for Seqan Massiv parallelization of Myers Fast Bit Vector Algorithm for Approximate String Matchinsg us…
ThesisMCRazer
in ABI
ThesisMCRazer Check, whether abstract, description, and literature are in CMS Parallelization of RazerS $ Student: Martin Riese $ Academic Advisor: David W…
ThesisMeganRazersReports
in ABI
Page ThesisMeganRazersReports Weekly Reports for the Bachelor Thesis "Comparative Genomics with MEGAN and RazerS" by Hannes Hauswedell Week 1 (2009 07 11..2009 0…
ThesisNGSOverlap
in ABI
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…
ThesisNgsCleaning
in ABI
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…
ThesisPalindromes
in ABI
Complemented palindromes Zusammenfassung Implementierung und Vergleich drei verschiedener Ansätze zum Finden von maximalen, komplementären Palindromen einer sign…
ThesisParallelismInSeqan
in ABI
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…
ThesisParallelismInSeqanPatterns
in ABI
Parallelism In The SeqAn Library: Patterns for Parallelization A brief summary of patterns for parallelization, based on Massingill et al. 2000 . Finding Concur…
ThesisParallelismInSeqanWeeklyReports
in ABI
Parallelism In The SeqAn Library: #8220;Weekly #8221; Reports Weekly reports about ThesisParallelismInSeqan. General * 05/08 #8211;05/11: * Work on pre…
ThesisParallelismInSeqanWorkSchedule
in ABI
Parallelism In The SeqAn Library: Schedule Tentative Schedule Tentative total: 25 weeks. Review of existing literature and other implementations (2 #8211;4 weeks…
ThesisScalingGenomeAlignment
in ABI
Scaling genome alignment to hundreds of genomes Topic With the rapid development of next generation sequencing technologies more and more genomes are being seque…
ThesisScoreMatrix
in ABI
Substitution Matrix Generation Algorithms This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn, sou…
ThesisSeqAnBlast
in ABI
BLAST Implementation in SeqAn Es soll ein BLASTX (Nukleotidsequenz 6 fach translatieren und gegen Proteindatenbank abgleichen) 'from scratch' für die SeqAn Bib…
ViralIntegration
in ABI
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 …
WebPreferences
in ABI
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…
WebStatistics
in ABI
Statistics for ABI Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: …
WeeklyReportDFG
in ABI
Weekly Report for the DFG project: Algorithm Engineering for High Throughput Sequencing Data Summarizes the weekly progress of the DFG project. Jul 2011 * 01….
Worklog_Hauswedell
in ABI
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…
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