Franssen 2011 P. sativum unigene

Overview
Analysis NameFranssen 2011 P. sativum unigene
Methodmira/tgicl (na)
SourceFranssen 2011 P. sativum unigene
Date performed2011-05-11

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 NameValue
Analysis unigene num reads2,209,735
Analysis unigene avg length487
Analysis unigene num clusters
Analysis unigene num singlets26,622
Analysis Typetripal_analysis_unigene
Analysis unigene nameFranssen 2011 P. sativum unigene
Analysis unigene num contigs42,000
Functional Annotation
  • 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%