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SEED is a sequence editor and pipeline for Windows XP/7
53 articles
Logo.png SEED is a free-to-use GUI-based sequence editor and pipeline providing access to internal functions as well as those performed by external software that is installed for full functionality (1). SEED was created to provide an intuitive interface for fast bioinformatic analysis of PCR amplicons on desktop computers according to the suggested workflow. The most recent 64-bit version allows comfortable work with up to 8 million sequences (~4 GB of data) on a standard personal computer with 8 GB RAM. SEED is especially suitable for sequential analysis of the sequences of PCR amplicons obtained by Illumina or 454-pyrosequencing, such as sequences of fungal ITS regions, bacterial 16S rDNA or other target genes. The program has a wide array of functions including editing of sequences and their titles, sorting, quality trimming, pair-end joining, grouping of sequences based on sequence motifs or sequence titles, batch processing of sequence groups, denoising, chimera removal, ITS extraction, sequence alignments and clustering, OTU table construction, construction of consensus sequences, creation of local databases for BLAST and searching either them or the whole NCBI, retrieval of taxonomical classification from the NCBI, calculation of diversity parameters and many more.
(1) Větrovský, T. and P. Baldrian (2013). "Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED." Biology and Fertility of Soils 49: 1027-1037.

Current version of SEED is 1.2.3