Difference between revisions of "Main Page"
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| − | + | SEED is a simple sequence editor and pipeline for processing of nucleotide sequences in the [//en.wikipedia.org/wiki/FASTA_format FASTA format]. SEED allows simple grouping of sequences based on the search for sequence motifs (e.g. primers, pyrosequencing tags) and a batch processing of the resulting groups. It also supports the connections to external tools for sequence processing and analysis like Mafft, Mothur, Uclust, Usearch, ITSx or Blast and can be used for further processing, visualization, management and analysis of their results. The SEED is especially designed to provide the environment for a sequential analysis of the sequences of PCR amplicons obtained by 454-pyrosequencing or Illumina. | |
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| + | Sequence editing and sorting// | ||
| + | Extraction of sequences and sequence qualities from *.sff files | ||
| + | Quality trimming | ||
| + | Grouping of sequences based on sequence motifs or sequence titles | ||
| + | Sequence batch processing | ||
| + | Sequence denoising (using PyroNoise algorithm translationAmpliconnoise within Mothur) | ||
| + | Chimera removal (using Uchime) | ||
| + | Sequence alignment (using MAFFT) | ||
| + | Sequence clustering (using Usearch) | ||
| + | Construction of consesus sequences | ||
| + | Searching best hits in local database or the NCBI (using nucleotide BLAST) | ||
| + | Retrieval of taxonomical classification of best hits from the NCBI | ||
| + | Creation of local databases for searching by nucleotide BLAST | ||
| + | Calculation of diversity parameters | ||
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. | Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. | ||
Revision as of 00:55, 5 March 2015
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SEED is a simple sequence editor and pipeline for processing of nucleotide sequences in the FASTA format. SEED allows simple grouping of sequences based on the search for sequence motifs (e.g. primers, pyrosequencing tags) and a batch processing of the resulting groups. It also supports the connections to external tools for sequence processing and analysis like Mafft, Mothur, Uclust, Usearch, ITSx or Blast and can be used for further processing, visualization, management and analysis of their results. The SEED is especially designed to provide the environment for a sequential analysis of the sequences of PCR amplicons obtained by 454-pyrosequencing or Illumina.
Sequence editing and sorting// Extraction of sequences and sequence qualities from *.sff files Quality trimming Grouping of sequences based on sequence motifs or sequence titles Sequence batch processing Sequence denoising (using PyroNoise algorithm translationAmpliconnoise within Mothur) Chimera removal (using Uchime) Sequence alignment (using MAFFT) Sequence clustering (using Usearch) Construction of consesus sequences Searching best hits in local database or the NCBI (using nucleotide BLAST) Retrieval of taxonomical classification of best hits from the NCBI Creation of local databases for searching by nucleotide BLAST Calculation of diversity parameters
Consult the User's Guide for information on using the wiki software.
