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  • 1
    Online Resource
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    Algorithms for molecular biology : AMB (2006)
    London : BioMed Central ; 1.2006 -
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    UID:
    (DE-627)508725755
    Format: Online-Ressource
    ISSN: 1748-7188
    Language: English
    Keywords: Zeitschrift
    URL: kostenfrei
    URL: https://ezb.ur.de/?2224970-9
    URL: kostenfrei
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    Stabi Berlin
    UB Potsdam
    BSZ
    ZDB
    GBV
  • 2
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    An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies (15)
    Details
    UID:
    (DE-627)1840592052
    Format: 12
    ISSN: 1748-7188
    Content: Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.
    Note: Gesehen am 30.03.2023
    In: Algorithms for molecular biology, London : BioMed Central, 2006, 5(2010), 1, Artikel-ID 29, Seite 1-12, 1748-7188
    In: volume:5
    In: year:2010
    In: number:1
    In: elocationid:29
    In: pages:1-12
    In: extent:12
    Language: English
    DOI: 10.1186/1748-7188-5-29
    URL: Volltext  (lizenzpflichtig)
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  • 3
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    DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment : Research (2008)
    Details
    UID:
    (DE-627)575629487
    Format: Online-Ressource (PDF-Datei: 11 S., 330 KB)
    ISSN: 1748-7188
    Content: Background: DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN-TX, a substantial improvement of DIALIGN-T that combines our previous greedy algorithm with a progressive alignment approach. Results: Our new heuristic produces significantly better alignments, especially on globally related sequences, without increasing the CPU time and memory consumption exceedingly. The new method is based on a guide tree; to detect possible spurious sequence similarities, it employs a vertex-cover approximation on a conflict graph. We performed benchmarking tests on a large set of nucleic acid and protein sequences For protein benchmarks we used the benchmark database BALIBASE 3 and an updated release of the database IRMBASE 2 for assessing the quality on globally and locally related sequences, respectively. For alignment of nucleic acid sequences, we used BRAliBase II for global alignment and a newly developed database of locally related sequences called DIRM-BASE 1. IRMBASE 2 and DIRMBASE 1 are constructed by implanting highly conserved motives at random positions in long unalignable sequences. Conclusion: On BALIBASE3, our new program performs significantly better than the previous program DIALIGN-T and outperforms the popular global aligner CLUSTAL W, though it is still outperformed by programs that focus on global alignment like MAFFT, MUSCLE and T-COFFEE. On the locally related test sets in IRMBASE 2 and DIRM-BASE 1, our method outperforms all other programs while MAFFT E-INSi is the only method that comes close to the performance of DIALIGN-TX.
    Note: Systemvoraussetzungen: Acrobat reader.
    In: Algorithms for molecular biology, London : BioMed Central, 2006, 3(2008), 6, Seite 1-11, 1748-7188
    In: volume:3
    In: year:2008
    In: number:6
    In: pages:1-11
    Language: English
    URL: Volltext
    URL: Volltext
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  • 4
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    An integrative approach for a network based meta-analysis of viral RNAi screens (13)
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    UID:
    (DE-627)1725358700
    Format: 15
    ISSN: 1748-7188
    Content: Big data is becoming ubiquitous in biology, and poses significant challenges in data analysis and interpretation. RNAi screening has become a workhorse of functional genomics, and has been applied, for example, to identify host factors involved in infection for a panel of different viruses. However, the analysis of data resulting from such screens is difficult, with often low overlap between hit lists, even when comparing screens targeting the same virus. This makes it a major challenge to select interesting candidates for further detailed, mechanistic experimental characterization.
    Note: Gesehen am 23.07.2020
    In: Algorithms for molecular biology, London : BioMed Central, 2006, 10(2015) Artikel-Nummer 6, 15 Seiten, 1748-7188
    In: volume:10
    In: year:2015
    In: extent:15
    Language: English
    DOI: 10.1186/s13015-015-0035-7
    URL: Volltext  (lizenzpflichtig)
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  • 5
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    Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tail : Research (2007)
    Details
    UID:
    (DE-627)560249446
    Format: Online-Ressource (PDF-Datei: 17 S., 619,09 KB)
    ISSN: 1748-7188
    Content: Background: The optimal score for ungapped local alignments of infinitely long random sequences is known to follow a Gumbel extreme value distribution. Less is known about the important case, where gaps are allowed. For this case, the distribution is only known empirically in the high-probability region, which is biologically less relevant. Results: We provide a method to obtain numerically the biologically relevant rare-event tail of the distribution. The method, which has been outlined in an earlier work, is based on generating the sequences with a parametrized probability distribution, which is biased with respect to the original biological one, in the framework of Metropolis Coupled Markov Chain Monte Carlo. Here, we first present the approach in detail and evaluate the convergence of the algorithm by considering a simple test case. In the earlier work, the method was just applied to one single example case. Therefore, we consider here a large set of parameters: We study the distributions for protein alignment with different substitution matrices (BLOSUM62 and PAM250) and affine gap costs with different parameter values. In the logarithmic phase (large gap costs) it was previously assumed that the Gumbel form still holds, hence the Gumbel distribution is usually used when evaluating p-values in databases. Here we show that for all cases, provided that the sequences are not too long (L 〉 400), a "modified" Gumbel distribution, i.e. a Gumbel distribution with an additional Gaussian factor is suitable to describe the data. We also provide a "scaling analysis" of the parameters used in the modified Gumbel distribution. Furthermore, via a comparison with BLAST parameters, we show that significance estimations change considerably when using the true distributions as presented here. Finally, we study also the distribution of the sum statistics of the k best alignments.
    Note: Systemvoraussetzungen: Acrobat reader.
    In: Algorithms for molecular biology, London : BioMed Central, 2006, 2(2007), 9, Seite 1-17, 1748-7188
    In: volume:2
    In: year:2007
    In: number:9
    In: pages:1-17
    Language: English
    URL: Volltext
    URL: Volltext
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  • 6
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    Multiple sequence alignment with user-defined anchor points (2006)
    Details
    UID:
    (DE-627)524837791
    Format: Online-Ressource (PDF-Datei: 12 S., 322,92)
    ISSN: 1748-7188
    Content: Background: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results: Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take re-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system.
    Note: Systemvoraussetzungen: Acrobat reader.
    In: Algorithms for molecular biology, London : BioMed Central, 2006, 1(2006), 6, Seite 1-12, 1748-7188
    In: volume:1
    In: year:2006
    In: number:6
    In: pages:1-12
    Language: English
    URL: Volltext
    URL: Volltext
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  • 7
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    New journal: Algorithms for Molecular Biology : Editorial (2006)
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    UID:
    (DE-627)526419849
    Format: Online-Ressource (PDF-Datei: 3 S., 178,79 KB)
    ISSN: 1748-7188
    Content: This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions.
    Note: Systemvoraussetzungen: Acrobat reader.
    In: Algorithms for molecular biology, London : BioMed Central, 2006, 1(2006), 1, Seite 1-3, 1748-7188
    In: volume:1
    In: year:2006
    In: number:1
    In: pages:1-3
    Language: English
    URL: Volltext
    URL: Volltext
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  • 8
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    P-value based visualization of codon usage data (2006)
    Details
    UID:
    (DE-627)524846367
    Format: Online-Ressource (PDF-Datei: 7 S., 1,90 MB)
    ISSN: 1748-7188
    Content: Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose a multidimensional scaling approach using a novel similarity measure for codon usage tables. Our probabilistic similarity measure is based on P-values derived from the wellknown chi-square test for comparison of two distributions. Experimental results on four microbial genomes indicate that the new method is well-suited for the analysis of horizontal gene transfer and translational selection. As compared with the widely-used correspondence analysis, our method did not suffer from outlier sensitivity and showed a better clustering of putative alien genes in most cases.
    Note: Systemvoraussetzungen: Acrobat reader.
    In: Algorithms for molecular biology, London : BioMed Central, 2006, 1(2006), 10, Seite 1-7, 1748-7188
    In: volume:1
    In: year:2006
    In: number:10
    In: pages:1-7
    Language: English
    URL: Volltext
    URL: Volltext
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