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1DLoadBalancingConceptualDraft
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...
r9 - 16 Sep 2010 - 19:15 by KonradRudolph
AdapterRemoval
template void remove(StringSet seq, StringSet qual, StringSet const adapter) { Align, ArrayGaps align; resize(rows(align), 2); for ...
NEW - 12 Jun 2013 - 12:09 by jsinger
AdvancedAlgorithms
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 ...
r65 - 23 Mar 2011 - 09:25 by DavidWeese
AssignmentWeek1
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...
r8 - 30 Apr 2012 - 12:57 by SandroAndreotti
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
BScBlastInSeqAnProject
Eine vergleichende Studie von BLAST Algorithmen Aufgabenstellung BLAST (Basic Local Alignment Tool) ist das bekannteste Programm zur Identifizierung von lokalen ...
r3 - 14 Jul 2013 - 23:16 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
BScParallelBamIOScheduleProject
BScParallelBamIOScheduleProject Implementation of parallel de /compression of BAM files Project Schedule Tasks 1) Extract the compression and decompression in...
r8 - 05 Feb 2014 - 07:16 by olfrik
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
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
BscSeqAn010Seeds
Implementing 01*0 seed search strategy using the bidirectional FM index in SeqAn Background Approximate string matching is an important subtask in many bioinform...
r3 - 25 Nov 2016 - 15:08 by cpockrandt
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
ChipSeq
ChIP Seq Motivanalyse Konzept Bei der ChIP Seq Analyse werden die genomweiten Bindungsstellen von Transkriptionsfaktoren dadurch identifiziert, dass man die Tran...
NEW - 29 Mar 2012 - 10:12 by KnutReinert
DCLoadBalancingConceptualDraft
Parallelism In The SeqAn Library: 1D Load Balancing With Divide Conquer: Conceptual Draft Related to 1DLoadBalancingConceptualDraft . This part looks at the ...
r2 - 09 Jul 2010 - 16:12 by KonradRudolph
DCStaticLoadBalancing
Parallelism In The SeqAn Library: 1D Load Balancing: Conceptual Draft forall(AlgorithmState state, DataSpec spec) if spec is a leaf then process(state...
NEW - 14 Jul 2010 - 09:34 by KonradRudolph
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
DfgWorkPackages
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 (...
NEW - 07 Jan 2010 - 09:03 by KnutReinert
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
Expose
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...
r7 - 27 May 2010 - 17:37 by RmaerkerUserTopic
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
FMIndexThesis
FM Index in Seqan
NEW - 30 Apr 2013 - 19:28 by jsinger
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
GenomeComparisonP4
Page GenomeComparisonP4 This is the project page of the Genome Comparison group. Students Mail an alle Gruppenmitglieder: AA2010SS GenComp bei lists.spline.de ...
r39 - 19 Jul 2010 - 18:50 by homilius
GenomicsLecture9Materials
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 ...
r2 - 18 Dec 2012 - 16:33 by KnutReinert
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
JMatch
In diesem Praktikum geht es um die Erstellung von Software, um die Bindungsstellen von Transkriptionsfaktoren in DNA Sequenzen zu identifizieren und die Auswirkun...
r2 - 13 Apr 2012 - 16:10 by BirteKehr
JournalClubWS11
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...
r25 - 16 Jul 2012 - 11:20 by KnutReinert
JournalClubWS13
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...
r22 - 07 Feb 2014 - 13:50 by dadi
KnimeSec
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 ...
r18 - 03 Jul 2013 - 09:54 by aiche
LaganHome
LaganHome Projektplanung und Umsetzung zur Implementierung von LAGAN Projektplan und Aufteilung 1. Start: Einlesen von FastA Dateien (Moritz) 2. Diese soll s...
r11 - 16 May 2013 - 18:20 by kiekemo
LaganSeqan2018
LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntni...
NEW - 13 Apr 2018 - 13:26 by jwinkler
LectureWiki
OUT OF USE! Go to: https://kvv.imp.fu berlin.de/portal/ * SS 2018 * PMSB SeqAn * SS 2017 * PMSB SeqAn * SS 2016 * Journal Club * ...
r40 - 01 Oct 2019 - 14:16 by KasseckeUserTopic
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
NormEditDist
PISB SeqAn Projekt Normalised Edit Distance Hintergrund: Normalisierte Edit Distanz Die Edit Distanz ist ein Standarddistanzmaß für Sequenzalignments, Mappings...
NEW - 15 Mar 2012 - 16:45 by KathrinTrappe
PMSB_Seqan_2010
Projektmanagement im Softwarebereich Seqan 2010 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di...
r9 - 23 Mar 2011 - 09:25 by DavidWeese
PMSB_Seqan_2011
Projektmanagement im Softwarebereich Seqan 2011 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di...
r9 - 15 Apr 2011 - 10:51 by BirteKehr
PMSB_Seqan_2012
Projektmanagement im Softwarebereich SeqAn 2012 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Teilnehmer Name...
r28 - 25 May 2012 - 10:41 by JochenSinger
PMSB_Seqan_2013
Projektmanagement im Softwarebereich SeqAn 2013 Dies ist die Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Alle Zeiten sind s.t. also w...
r47 - 11 May 2015 - 10:43 by kiekemo
PMSB_Seqan_2014
Projektmanagement im Softwarebereich, SoSe 2014 (19588a und 19588b) * Einführung in Software Engineering am Freitag entfällt leider! Dies ist die Wiki Seite z...
r23 - 23 Apr 2014 - 08:58 by holtgrew
PMSB_Seqan_2015
Projektmanagement im Softwarebereich, SoSe 2015 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" Se...
r17 - 27 Mar 2015 - 09:37 by ReinertUserTopic
PMSB_Seqan_2016
Projektmanagement im Softwarebereich, SoSe 2016 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" S...
r18 - 11 Apr 2016 - 15:30 by h4nn3s
PMSB_Seqan_2017
Projektmanagement im Softwarebereich, SoSe 2017 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" S...
r2 - 27 Jan 2017 - 11:45 by h4nn3s
PMSB_Seqan_2018
Projektmanagement im Softwarebereich, SoSe 2018 Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" SeqAn für BSc Studenten. Alle Z...
r16 - 28 May 2018 - 13:57 by h4nn3s
PSMB_Seqan_2013_BlastX
Page PSMB_Seqan_2013_BlastX Hintergrund: NGS Daten in Proteindatenbanken Next Generation Sequencing (NGS) Daten werden heute für unterschiedlichste Aufgaben verw...
r8 - 28 May 2013 - 17:48 by marjan
PSMB_Seqan_2013_Lagan
Page PSMB_Seqan_2013_Lagan Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntniss...
r4 - 25 Apr 2013 - 09:34 by RmaerkerUserTopic
PSMB_Seqan_2013_NGS_Data_Cleansing
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver...
r2 - 12 Apr 2013 - 11:14 by lkuchenb
PSMB_Seqan_2013_NGS_Data_Cleansing_New
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver...
r2 - 12 Apr 2013 - 10:27 by lkuchenb
PSMB_Seqan_2013_NGS_Quality_Control
Page PSMB_Seqan_2013_NGS_Quality_Control Hintegrund: NGS Quality Control Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichne...
r6 - 19 Apr 2013 - 06:59 by olfrik
PSMB_Seqan_2013_NGS_Quality_Control_Details_Features
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...
r3 - 25 Apr 2013 - 12:00 by dkersting
PSMB_Seqan_2013_PEMer
Page PSMB_Seqan_2013_PEMer PEMer overview, Figure 1 from (Korbel et al., 2009). Hintergrund: Paired End Signaturen und Strukturvarianten Als Strukturvarianten be...
r7 - 07 May 2013 - 12:32 by zer
PSMB_Seqan_2013_Suboptimal_Alignments
Page PSMB_Seqan_2013_Suboptimal_Alignments Hintergrund: Suboptimale Alignments Lokale Alignments sind eine mächtige Methode um Sequenzhomologien zwischen zwei Se...
r2 - 01 Feb 2013 - 10:46 by ReneMaerker
PSMB_Seqan_2013_UBlast
Schnelle Blastsuche durch Datenbank Clustering Hintergrund: Der Vergleich von Next Generation Sequencing (NGS) Daten gegen DNA oder Proteindatenbanken gehoert ...
r3 - 12 Apr 2013 - 14:13 by lkuchenb
PSMB_Seqan_2014_SNP_caller
PSMB_Seqan_2014_SNP_caller Hintergrund Die häufigste und kleinste mögliche genomische Variation ist der Single Nucleotide Polymorphism. Nach dem Mapping von Read...
r8 - 10 Apr 2014 - 15:54 by sabrina7
PSMB_Seqan_2014_large_insertd
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...
r6 - 12 May 2014 - 08:59 by jobau
PSMB_Seqan_2014_mapper
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...
r5 - 21 Apr 2014 - 12:16 by RmaerkerUserTopic
PSMB_Seqan_2014_overview
PSMB_Seqan_2014_overview Im PSMB SeqAn 2014 geht es darum, eine einfach Pipeline zur Variantenanalyse aufzubauen. Hintergrund Insbesondere für das menschliche Ge...
NEW - 19 Mar 2014 - 11:19 by holtgrew
PSMB_Seqan_2014_small_indels
PSMB_Seqan_2014_small_indels Hintergrund Neben SNPs sind kleine Insertionen und Deletionen (indels) eine Klasse wichtiger genomischer Varianten. Für die Suche so...
r5 - 16 Apr 2014 - 14:39 by jsinger
PSMB_Seqan_2015_p2
Page PSMB_Seqan_2015_p2 Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse b...
NEW - 12 Mar 2015 - 18:01 by RmaerkerUserTopic
PSMB_Seqan_2015_p3
PSMB_Seqan_2015_p3 Einleitung Eines der bekanntesten und meist genutzten Programme im Kontext der Bioinformatik ist NCBI Blast. Blast ist ein heuristisches Tool ...
r4 - 13 Apr 2015 - 14:48 by h4nn3s
PSMB_Seqan_2015_p4
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 ...
r3 - 01 Apr 2015 - 14:48 by esiragusa
PSMB_Seqan_2015_p5
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...
r12 - 26 Mar 2015 - 19:34 by CxpanUserTopic
PSMB_Seqan_2015_palign
PSMB_Seqan_2015_palign Einleitung Paarweise Sequenzalignments liefern wertvolle biologische Informationen über die Identität zweier Sequenzen. Entsprechend w...
NEW - 12 Mar 2015 - 18:01 by RmaerkerUserTopic
PSMB_Seqan_2016_p1
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...
NEW - 26 Jan 2016 - 16:41 by h4nn3s
PSMB_Seqan_2016_p2
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...
r3 - 27 Jan 2016 - 19:16 by kjk
PSMB_Seqan_2016_p3
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...
r2 - 04 May 2016 - 13:52 by cpockrandt
PSMB_Seqan_2016_p4
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"...
r2 - 28 Jan 2016 - 18:04 by h4nn3s
PSMB_Seqan_2016_p5
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...
r2 - 28 Jan 2016 - 17:35 by dadi
PSMB_Seqan_2016_p6
LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntni...
r2 - 02 Feb 2018 - 09:27 by ReinertUserTopic
PSMB_Seqan_2017_p1
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...
NEW - 08 Feb 2017 - 11:28 by kjk
PSMB_Seqan_2017_webassembly
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...
NEW - 01 Feb 2018 - 14:32 by h4nn3s
PSMB_Seqan_IBF
Auswertugn von Binning directories mit Hilfe von Interleaved Bloom filters Hintergrund: Filtern von NGS reads in bins In dem projekt soll (zufällig generierte) ...
r2 - 02 Feb 2018 - 09:43 by ReinertUserTopic
PSMB_Seqan_MF
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...
r2 - 02 Feb 2018 - 09:25 by ReinertUserTopic
PSMB_Seqan_fft
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...
r2 - 13 Feb 2018 - 16:00 by troja
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
ProgressReportEmde-04-2010
Page ProgressReportEmde 04 2010 Progress report Accomplishments in the last six months: General: * Read many papers on variant detection, notes taken here. ...
r2 - 15 Apr 2010 - 13:30 by KnutReinert
ProgressReportEmde-05-2011
Page ProgressReportEmde 05 2011 Progress Report (under construction) Accomplishments in the last six months: SplazerS: * redid single end read simulation (co...
r5 - 31 May 2011 - 17:02 by KnutReinert
ProgressReportEmde-10-2010
Page ProgressReportEmde 10 2010 Progress Report Accomplishments in the last six months: Split read mapping: * Finished implementation of splitRazers, poster...
r6 - 18 May 2011 - 12:01 by AnneKatrinEmde
ProgressReportHu
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...
r5 - 30 Jan 2013 - 16:36 by BodoRiedigerKlaus
ProgressReportSiragusaFall2010
Page ProgressReportSiragusaFall2010 This is the progress report of Enrico Siragusa for the Fall 2010. Accomplishments up to the Fall 2010 * Familiarized with ...
r5 - 07 Dec 2010 - 13:38 by EnricoSiragusa
Projektseminar_Advanced_Sequence_Analysis_2013
Praxismodule Applied Sequence Analysis Welcome to the Wiki of the Praxisseminar Applied Sequence Analysis News Times and rooms Rooms and timings Event ...
r11 - 30 May 2013 - 11:29 by aiche
QualityTrim
//
================================================================ // quality_trimmer // ===================================...r2 - 12 Jun 2013 - 09:24 by jsinger
QuantProtP4_AMS
AMS 3.0 predicting post translational modification sites Material Paper http://www.biomedcentral.com/1471 2105/11/210/abstract OpenMS docu: http://www bs2....
r5 - 22 Jun 2010 - 13:59 by ChrisBielow
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
Razers2Revision
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...
r33 - 03 Jul 2012 - 09:26 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
Reads
reads.fastq This page contains the read.fastq file
NEW - 04 Jun 2013 - 10:56 by jsinger
RepeatMasking
Repeat Masking Repeats in DNA Sequenzen sind ein häufig beobachtetes Phänomen. Insbesondere in den ersten Schritten der Genome Analyse verursachen sie Probleme, d...
r5 - 13 Apr 2012 - 15:11 by JochenSinger
ResearchCooperations
Research Cooperations The Reinert group at FU Berlin maintains research cooperations with German and international research groups. Note that this list here is no...
NEW - 06 May 2011 - 10:31 by ManuelHoltgrewe
ResearchLogTemesgenDadi18032014
Meeting/Consultation minute 18 03 2014 Discussed Topics: * Genovo: Genovo is written in C . * Other metagenomic assemblers: Metavelvet, an extension of...
NEW - 20 Mar 2014 - 09:12 by dadi
ResearchLogs
Research Logs * Genome Comparison (Birte Kehr, Manuel Holtgrewe) * Precursor Selection (Alexandra Zerck) * Indices and Applications (David Weese) * BW...
r8 - 20 Oct 2014 - 16:16 by CxpanUserTopic
RnaSeqMSplazers
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...
r2 - 18 Apr 2012 - 16:40 by KathrinTrappe
RnaSeqP4
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...
r51 - 22 Jul 2010 - 16:30 by cblasse
RnaSeqReadSimulator
PISB SeqAn RNA Seq Read Simulator Hintergrund: RNA Seq Simulation Simulierte Daten leisten wichtige Dienste bei der Entwicklung, Fehlersuche und Bewertung von ...
r2 - 12 Apr 2012 - 14:07 by ManuelHoltgrewe
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
SegementAligner
PISB SeqAn Teilprojekte Segment Aligner Hintergrund: Hierarchisches Genomalignment Um das Alignment ganzer Genome zu ermöglichen, werden in der Regel zunächst ...
r3 - 13 Mar 2012 - 14:31 by BirteKehr
SeqAnRetreat2010
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...
r11 - 06 May 2011 - 00:57 by ManuelHoltgrewe
SeqAnRetreat2011
Information about the SeqAn workshop 2011 The SeqAn BioStore website is up. Please find information here.
r8 - 14 Jul 2011 - 22:40 by KnutReinert
SeqAnRetreat2012
Guidelines for the Organization of Meetings Technical Factors * find/reserve a room SeqAn Retreat March 2012 with Illumina: T9/053 * look into technical...
NEW - 29 Feb 2012 - 18:04 by AnjaKasseckert
Sequence_analysis_2014
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...
r32 - 12 Jul 2014 - 15:18 by ReinertUserTopic
Sequence_analysis_2015
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...
r38 - 07 Jul 2015 - 11:59 by RmaerkerUserTopic
Sequence_analysis_2016
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...
r3 - 04 Mar 2016 - 15:24 by ReinertUserTopic
SimpleBowtie
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...
r4 - 30 Mar 2012 - 13:32 by KnutReinert
SlaganSupermap
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...
r11 - 12 Jul 2010 - 13:57 by heeger
SnippetsAnneKatrin
Page SnippetsAnneKatrin This is where I write my weekly goals. all time todos: * make splitRazers project page * add link in seqanswers forum srp thread ...
r34 - 07 Dec 2010 - 13:43 by AnneKatrinEmde
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
SpecificationsAR
Write a SeqAn program that: * reads in....
NEW - 30 May 2013 - 10:48 by ReinertUserTopic
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
StellarMotifFinderWeeklyReports
Page StellarMotifFinderWeeklyReports These are brief weekly reports about the status of the BSc Thesis StellarMotifFinder. Week 1 (25.07.2012 31.07.2012) * ...
r4 - 31 Aug 2012 - 09:46 by shalini6
StellarTuning
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...
r2 - 28 Mar 2012 - 14:01 by ManuelHoltgrewe
StundenPlan
StundenPlan Reinert / Piro / Marsico SoSe 2017 time: Monday Tuesday Wednesday Thursday Friday 8 10 10 12 SeqAnalys (VL) 051/t9 ...
r7 - 21 Feb 2018 - 12:54 by KasseckeUserTopic
ThesesHome
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...
r108 - 23 Sep 2019 - 11:22 by KasseckeUserTopic
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
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
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
ThesisMeganRazersReports
Page ThesisMeganRazersReports Weekly Reports for the Bachelor Thesis "Comparative Genomics with MEGAN and RazerS" by Hannes Hauswedell Week 1 (2009 07 11..2009 0...
r9 - 29 Sep 2009 - 21:55 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
ThesisParallelismInSeqanPatterns
Parallelism In The SeqAn Library: Patterns for Parallelization A brief summary of patterns for parallelization, based on Massingill et al. 2000 . Finding Concur...
r12 - 21 Jun 2010 - 15:37 by KonradRudolph
ThesisParallelismInSeqanWeeklyReports
Parallelism In The SeqAn Library: #8220;Weekly #8221; Reports Weekly reports about ThesisParallelismInSeqan. General * 05/08 #8211;05/11: * Work on pre...
r26 - 29 Nov 2010 - 10:05 by KonradRudolph
ThesisParallelismInSeqanWorkSchedule
Parallelism In The SeqAn Library: Schedule Tentative Schedule Tentative total: 25 weeks. Review of existing literature and other implementations (2 #8211;4 weeks...
r9 - 14 Jul 2010 - 09:33 by KonradRudolph
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
ViralIntegration
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 ...
r12 - 18 Jul 2010 - 12:29 by cblasse
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: ...
r607 - 11 May 2025 - 04:03 by AdminUser
WeeklyReportDFG
Weekly Report for the DFG project: Algorithm Engineering for High Throughput Sequencing Data Summarizes the weekly progress of the DFG project. Jul 2011 * 01....
r8 - 05 Sep 2011 - 10:19 by ReneMaerker
Worklog_Hauswedell
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...
r4 - 06 Jul 2010 - 19:16 by h4nn3s
Number of topics: 144
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