Computational protocol: Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal

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Protocol publication

[…] Sequences from isolated bands were verified and aligned using BioEdit version 7.1.3.0 [] and analyzed along with sequences obtained from DDBJ/EMBL/GenBank International Nucleotide Sequence Database. For sequence similarity analyses Clustal W2 [] was used.Inter Retrotransposons Amplified Polymorphism (IRAP), Retrotransposons Microsatellite Amplified Polymorphism (REMAP) and centromeric sequences PCR banding profiles obtained were transformed in binary matrices, where 1 corresponds to band presence and 0 to absence. NTSYSpc software [] was used to infer genetic similarity between all accessions and species using Dice coefficient []. Dendrograms were obtained through UPGMA (Unweighted Pair Group Method with Arithmetic Mean) method for a concatenated binary of CCS1, IRAP and REMAP profiles obtained using Concatenator Software []. Cophenetic correlation coefficient (r) was estimated to verify the adjustment between similarity matrix and respective dendrogram-derived matrix. The determination of confidence limits by bootstrap analysis was done using the WINBOOT software. […]

Pipeline specifications

Software tools BioEdit, Clustal W, NTSYSpc
Databases DDBJ
Application Population genetic analysis
Organisms Secale cereale, Avena sativa