pp-Blast: a "pseudo-parallel" Blast

Osório, Elisson C.; Souza, J.E. de; Zaiats, André C.; Oliveira, Paula; Souza, Sandro J. de

doi:10.1590/s0100-879x2003000400007

Cited by 5 publications

(1 citation statement)

References 3 publications

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“…All human cDNAs available in dbEST (July 2002, Ref. 4) and mRNA sequences from known human genes from UniGene release 153 (29) were aligned to the masked human genome sequence [build 29, obtained from the National Center for Biotechnology Information (NCBI)] by use of pp-Blast (27), an implementation of MEGABLAST (37) for a parallel cluster. The parameters used in MEGABLAST were: Ϫf T ϪJ F ϪF F ϪW 24.…”

Section: Methodsmentioning

confidence: 99%

Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data

Kirschbaum-Slager

Parmigiani

Camargo

et al. 2005

Physiological Genomics

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2004.-Alternative splicing is one of the major sources of the large transcriptional diversity found in human cells. Splicing variants have been shown to be associated with features like spreading and progression in several human tumors. Therefore, such variants may be of great importance as both diagnostic and therapeutic tools. Here, by using a set of criteria regarding the expression pattern of splicing variants and statistical analyses, we were able to screen the genome for exons overexpressed in tumors of specific tissues. However, as in other analyses attempting to identify tumor-associated variants, our list of candidates was seriously inflated with cases of genes differentially expressed in tumors. To exclude these cases and increase the probability of finding bona fide regulated splicing variants, we performed a serial analysis of gene expression (SAGE), excluding those genes that were shown to be upregulated in tumors. This allowed us to predict the overexpression of single exons in specific tumors. Our final group of candidates includes 1,386 exons belonging to 638 genes. Experimental validation of a few candidates in normal tissue, tumor cell lines, and patient samples suggests that most of these candidates are indeed tumor-associated exons. Further functional classification of our candidate genes shows that our final list is slightly inflated with cancer-related genes. alternative splicing; tumor; transcriptome; serial analysis of gene expression ALTERNATIVE SPLICING is one of the main sources of the variability found in the human transcriptome (3). There are four different types of alternative splicing: exon skipping/usage, alternative usage of a donor site, alternative usage of an acceptor site, and intron retention (20). Several bioinformatics analyses have indicated that at least one-half of all human genes undergo alternative splicing (7,11,17,22,23). In roughly 80% of these cases, alternative splicing invokes changes in the coding region (CDS) of genes, resulting in structural changes of the respective protein product (14, 23).The biological impact of alternative splicing is perceptible, for example, in Drosophila, in which sex determination is triggered by alternative splicing of a master gene (25). Furthermore, ϳ15% of all human genetic diseases are believed to be caused by mutations in the splicing acceptor/donor sites, generating changes in the splicing pattern of one or more genes, which implies that alternative splicing also plays an important role in pathogenicity (19).An apparent link between certain cancer types and alternative splicing is being investigated (for a review, see Caballero et al., Ref. 8). Several splicing variants from different genes, including cd44, wt1, cd79b, bin1, and Syk, have been shown to be associated with different aspects of tumorigenesis (1, 10,13,26,32).The increasing amount of cDNA libraries constructed from a diversity of both tumor and normal tissues and cell lines allows several types of computational analyses. This, together with the release of the fina...

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Section: Methodsmentioning

confidence: 99%

Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data

Kirschbaum-Slager

Parmigiani

Camargo

et al. 2005

Physiological Genomics

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Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis

Bettoni¹,

Filho²,

Grosso³

et al. 2009

Genomics

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Cancer/testis Antigens (CTAs) are immunogenic proteins with a restricted expression pattern in normal tissues and aberrant expression in different types of tumors being considered promising candidates for immunotherapy. We used the alignment between EST sequences and the human genome sequence to identify novel CT genes. By examining the EST tissue composition of known CT clusters we defined parameters for the selection of 1184 EST clusters corresponding to putative CT genes. The expression pattern of 70 CT gene candidates was evaluated by RT-PCR in 21 normal tissues, 17 tumor cell lines and 160 primary tumors. We were able to identify 4 CT genes expressed in different types of tumors. The presence of antibodies against the protein encoded by 1 of these 4 CT genes (FAM46D) was exclusively detected in plasma samples from cancer patients. Due to its restricted expression pattern and immunogenicity FAM46D represents a novel target for cancer immunotherapy.

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A Parallel Pairwise Local Sequence Alignment Algorithm

Bandyopadhyay

Mitra

2009

IEEE Trans.on Nanobioscience

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Researchers are compelled to use heuristic-based pairwise sequence alignment tools instead of Smith-Waterman (SW) algorithm due to space and time constraints, thereby losing significant amount of sensitivity. Parallelization is a possible solution, though, till date, the parallelization is restricted to database searching through database fragmentation. In this paper, the power of a cluster computer is utilized for developing a parallel algorithm, RPAlign, involving, first, the detection of regions that are potentially alignable, followed by their actual alignment. RPAlign is found to reduce the timing requirement by a factor of upto 9 and 99 when used with the basic local alignment search tool (BLAST) and SW, respectively, while keeping the sensitivity similar to the corresponding method. For distantly related sequences, which remain undetected by BLAST, RPAlign with SW can be used. Again, for megabase-scale sequences, when SW becomes computationally intractable, the proposed method can still align them reasonably fast with high sensitivity.

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pp-Blast: a "pseudo-parallel" Blast

Cited by 5 publications

References 3 publications

Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data

Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data

Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis

A Parallel Pairwise Local Sequence Alignment Algorithm

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