When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/

https://journal.embnet.org/index.php/embnetjournal/article/download/200/458

Cutadapt removes adapter sequences from high-throughput sequencing reads

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideration. Furthermore, the linear order of these segments may be shuffled among genomes. We present methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.

/pdf/mauve-multiple-alignment-of-conserved-genomic-sequence-with-5f3czjsw6r.pdf

Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Describing algorithms in a C-like language, this text presents examples related to the automatic processing of natural language, to the analysis of molecular sequences and to the management of textual databases.

/pdf/algorithms-on-strings-4gb4kbks4k.pdf

Algorithms on Strings

New updated! The latest book from a very famous author finally comes out. Book of handbook of exact string matching algorithms, as an amazing reference becomes what you need to get. What's for is this book? Are you still thinking for what the book is? Well, this is what you probably will get. You should have made proper choices for your better life. Book, as a source that may involve the facts, opinion, literature, religion, and many others are the great friends to join with.

Handbook of Exact String Matching Algorithms

We show how to speed up two string-matching algorithms: the Boyer-Moore algorithm (BM algorithm), and its version called here the reverse factor algorithm (RF algorithm). The RF algorithm is based on factor graphs for the reverse of the pattern. The main feature of both algorithms is that they scan the text right-to-left from the supposed right position of the pattern. The BM algorithm goes as far as the scanned segment (factor) is a suffix of the pattern. The RF algorithm scans while the segment is a factor of the pattern. Both algorithms make a shift of the pattern, forget the history, and start again. The RF algorithm usually makes bigger shifts than BM, but is quadratic in the worst case. We show that it is enough to remember the last matched segment (represented by two pointers to the text) to speed up the RF algorithm considerably (to make a linear number of inspections of text symbols, with small coefficient), and to speed up the BM algorithm (to make at most 2 ·n comparisons). Only a constant additional memory is needed for the search phase. We give alternative versions of an accelerated RF algorithm: the first one is based on combinatorial properties of primitive words, and the other two use the power of suffix trees extensively. The paper demonstrates the techniques to transform algorithms, and also shows interesting new applications of data structures representing all subwords of the pattern in compact form.

/pdf/speeding-up-two-string-matching-algorithms-4554ssggk6.pdf

Speeding up two string-matching algorithms

This article addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to such diverse areas as text, image and signal processing, speech analysis and recognition, information retrieval, data compression, computational biology and chemistry.In the last decade more than 50 new algorithms have been proposed for the problem, which add up to a wide set of (almost 40) algorithms presented before 2000. In this article we review the string matching algorithms presented in the last decade and present experimental results in order to bring order among the dozens of articles published in this area.

Thierry Lecroq

Papers

Algorithms on Strings

Handbook of Exact String Matching Algorithms

Speeding up two string-matching algorithms

The exact online string matching problem: A review of the most recent results

Algorithms on Strings: Tools