<i>De novo</i> transcriptome analysis by deep RNA sequencing
Bibliographic Information
- Other Title
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- 次世代シーケンサーを用いた<i>de novo </i>トランスクリプトーム解析
- 次世代シーケンサーを用いたde novoトランスクリプトーム解析
- ジセダイ シーケンサー オ モチイタ de novo トランスクリプトーム カイセキ
- De novo transcriptome analysis by deep RNA sequencing
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Abstract
For researchers using non-model animal species, we here introduce the method of de novo transcriptome sequencing using Illumina short read data at a low cost. Sequence assembly without a reference genome is called de novo assembly. The absence of genome information has been a large disadvantage for transcriptome sequencing of non-model animals, because it makes transcriptome assembly difficult. The present technical note describes how to prepare the RNA sample, perform a deep RNA sequencing and de novo assembly. For de novo assembly, five assembly programs are compared: ABySS, Velvet, OASES, Trinity and Rnnotator. We also show how to classify the obtained sequences associated with gene ontology (GO) terms at the protein level annotation using BLAST2GO program. We hope this technical note will help the researchers to start a transcriptome analysis and facilitate the future genetic analysis of non-model animal.
Journal
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- Hikaku seiri seikagaku(Comparative Physiology and Biochemistry)
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Hikaku seiri seikagaku(Comparative Physiology and Biochemistry) 29 (3), 131-134, 2012
THE JAPANESE SOCIETY FOR COMPARATIVE PHYSIOLOGY AND BIOCHEMISTRY
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Details 詳細情報について
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- CRID
- 1390001204669016448
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- NII Article ID
- 10031123312
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- NII Book ID
- AN10391932
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- ISSN
- 18819346
- 09163786
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- NDL BIB ID
- 024013957
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- Text Lang
- ja
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- Data Source
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- JaLC
- NDL
- Crossref
- CiNii Articles
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- Abstract License Flag
- Disallowed