Franssen 2011 P. sativum unigene

Overview
Analysis NameFranssen 2011 P. sativum unigene
Unigene NameFranssen 2011 P. sativum unigene
Methodmira/tgicl (na)
SourceFranssen 2011 P. sativum unigene
Date performed2011-05-11
Number of Reads2,209,735
Number of Contigs42,000
Number of Singlets26,622
OrganismsPisum sativum

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.

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%