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Overview
| Analysis Name | Franssen 2011 P. sativum unigene |
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| Method | mira/tgicl (na) |
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| Source | Franssen 2011 P. sativum unigene |
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| Date performed | 2011-05-11 |
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81,449 unigenes (Franssen et al 2011) were provided from assembly of 2,209,735 transcripts generated from 454 sequencing of Pisum sativum libraries from flowers, leaves, cotyledons, epi- and hypocotyl, and etiolated and light treated etiolated seedlings. For the CSFL version of the data, sequences less than 100 bp were removed from the assembly which resulted in 42,000 contigs and 26,622 singlets. The unigenes (contigs and singlets) were then analyzed using the annotation pipeline stated in the 'Functional Annotation' section.
Properties
Additional information about this analysis:
| Property Name | Value |
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| Analysis unigene num reads | 2,209,735 |
| Analysis unigene avg length | 487 |
| Analysis unigene num singlets | 26,622 |
| Analysis unigene num clusters | |
| Analysis unigene name | Franssen 2011 P. sativum unigene |
| Analysis unigene num contigs | 42,000 |
| Analysis Type | tripal_analysis_unigene |
Download
Unigene Files:
Homology Analysis Reports:
Microsatelite Analysis:
Functional Analysis
- Homology Analysis:
The unigenes were compared to the Uniprot Swissprot and Uniprot TrEMBL databases using the NCBI blastx program with E-value threshold of 1E-6. The results were generated in XML format and parsed into the database for online display. An in-house script was used to generate the best hit reports from the XML output which can be downloaded in Excel file format.
- InterproScan:
The unigenes were scanned for protein signatures and domains using the EBI InterproScan software (version 4.7) installed on-site. IPR terms and GO terms were generated for the analyzed sequences (i.e. parameters used: -iprlookup -goterms -format html -nocrc).
- KEGG/KASS:
The unigenes were submitted to the KAAS (KEGG Automatic Annotation Server) for ortholog assignment and pathway mapping. Five plant transcriptomes (i.e. Arabidopsis thaliana, Oryza sativa japonica, Ostreococcus lucimarinus, Ostreococcus tauri, Cyanidioschyzon merolae) were compared using the BBH method.
Microsatelite Analysis
The unigene contigs were scanned for microsatelites (SSR). SSRs are defined as dinucleotides repeated at least 5 times, trinucleotides repeated at least 4 times, tetranucleotides repeated at least 3 times, or pentanucleotides repeated at least 3 times.
| Sequence information |
| Number of Sequences |
42,000 |
| Number of Sequences Having One Or More SSRs |
5,095 |
| Percentage of Sequences Having One Or More SSRs |
12.1% |
| Total Number of SSRs Found |
10,286 |
| Number of Motifs |
474 |
Frequency of Motif Type
| Motif Length |
Frequency |
Percentage Frequency |
| 2bp |
1,140 |
17.8% |
| 3bp |
3,362 |
52.5% |
| 4bp |
1,461 |
22.8% |
| 5bp |
445 |
6.9% |
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