EST Pipeline System: Detailed and Automated EST Data Processing and Mining

Xu, Hao; He, Ling; Zhu, Yuanzhong; Huang, Wei; Fang, Lijun; Lin, Tao; Zhu, Yue-Dong; Cai, Lin; Xu, Huayong; Zhang, Liang; Yu, Hong; Zhou, Yan

doi:10.1016/s1672-0229(03)01029-5

Cited by 13 publications

(10 citation statements)

References 14 publications

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“…A number of standalone software packages are available for EST data analysis [26][27][28][29][30][31][32][33][34][35][36][37]. However, those programs require researchers to install and maintain the software locally, which many biologists find inconvenient (e.g., certain prerequisites can present a serious challenge to install and update, even for bioinformaticians).…”

Section: Comparison With Other Existing Est Analysis Programsmentioning

confidence: 99%

ESTPiper – a web-based analysis pipeline for expressed sequence tags

et al. 2009

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Background: EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components.

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Section: Comparison With Other Existing Est Analysis Programsmentioning

confidence: 99%

ESTPiper – a web-based analysis pipeline for expressed sequence tags

et al. 2009

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“…Sequence edit and analysis were performed using the program EST Analysis Pipeline System (Xu et al 2003). DNA sequences longer than 100 bases were analysed by comparison with data deposited in the GenBank database (http://www.ncbi.nih.gov) using the BLAST algorithm (Altschul, Gish, Miller, Myers & Lipman 1990).…”

Section: Fosmid Library Construction and Quality Detectionmentioning

confidence: 99%

Sequence analysis of Arthrospira maxima based on fosmid library

et al. 2007

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is an important cyanobacterium not only in its nutritional potential but in its special biological characteristics. An unbiased fosmid library of Arthrospira maxima FACHB438 that contains 4300 clones was constructed. The size distribution of insert fragments is from 15.5 to 48.9 kb and the average size is 37.6 kb. The recombination frequency is 100%. Therefore the library is 29.9 equivalents to the Arthrospira genome size of 5.4 Mb. A total of 719 sample clones were randomly chosen from the library and 602 available sequences, which consisted of 307,547 bases, covering 5.70% of the whole genome. The codon usage of A. maxima was not strongly biased. GC content at the first position of codons (46.9%) was higher than the second (39.8%) and the third (45.5%) positions. GC content of the genome was 43.6%. Of these sequences, 287 (47.7%) showed high similarities to known genes, 63 (10.5%) to hypothetical genes and the remaining 252 (41.8%) had no significant similarities. The assigned genes were classified into 22 categories with respect to different biological roles. Remarkably, the high presence of 25 sequences (4.2%) encoding reverse transcriptase indicates the RT gene may have multiple copies in the A. maxima genome and might play an important role in the evolutionary history and metabolic regulation. In addition, the sequences encoding the ATP-binding cassette transport system and the two-component signal transduction system were the second and third most frequent genes, respectively. These genomic features provide some clues as to the mechanisms by which this organism adapts to the high concentration of bicarbonate and to the high pH environment.

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“…Several EST processing systems have been developed to cope with these challenges such as EST analysis pipeline (ESTAP) (7), ESTAnnotator (8), EST pipeline system (9), PartiGene (10) and ParPEST (11). Although they each have their own objectives, these systems commonly provide automated or semi-automated pipelines for cleansing EST sequences and annotating them using public databases (12).…”

Section: Introductionmentioning

confidence: 99%

ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences

Lee

Hong

Byun

et al. 2007

Nucleic Acids Research

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We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass accepts a FASTA-formatted EST file and its quality file as inputs, and it then executes a back-end EST analysis pipeline consisting of three consecutive steps. The first is cleansing the input EST sequences. The second is clustering and assembling the cleansed EST sequences using d2_cluster and CAP3 programs and producing putative transcripts. From the CAP3 output, ESTpass detects chimeric EST sequences which are confirmed through comparison with the nr database. The last step is annotating the putative transcript sequences using RefSeq, InterPro, GO and KEGG gene databases according to user-specified options. The major advantages of ESTpass are the integration of cleansing and annotating processes, rigorous chimeric EST detection, exhaustive annotation, and email reporting to inform the user about the progress and to send the analysis results. The ESTpass results include three reports (summary, cleansing and annotation) and download function, as well as graphic statistics. They can be retrieved and downloaded using a standard web browser. The server is available at http://estpass.kobic.re.kr/.

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EST Pipeline System: Detailed and Automated EST Data Processing and Mining

Cited by 13 publications

References 14 publications

ESTPiper – a web-based analysis pipeline for expressed sequence tags

ESTPiper – a web-based analysis pipeline for expressed sequence tags

Sequence analysis of Arthrospira maxima based on fosmid library

ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences

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