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DbDesc will use XSLT templates to transform a XML file which holds your database description to get the final documentation. Advertisements DbDesc is a powerful tool to help you document your databases.
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If you continue browsing, you are considered to have accepted such use. CD-HIT: accelerated for clustering the next generation sequencing data. For example, at UniProt, CD-HIT is used to generate the UniRef reference data sets (http://www.Pir.Uniprot.Org/database/DBDescription.Shtml). Our antivirus check shows that this download is malware free. CD-HIT-2D (CD-HIT-EST-2D) can compare two databases uploaded by users.
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ScreenShot Review this Software Name * Email * Website Comment You may use these HTML tags and attributes: Review this Software Name * Email * Website Comment You may use these HTML tags and attributes: June 18 We have fixed our email. Basic command: Choose of word size: More options: Options, -b, -M, -l, -d, -t, -s, -S, -B, -p, -aL, -AL, -aS, -AS, -g, -G, -T are same to CD-HIT, here are few more cd-hit-est specific options: CD-HIT-EST-2D compares 2 nucleotide datasets (db1, db2). BMC Bioinformatics, (2010) 11:187 PDF Pubmed Clustering a sequence database requires all-by-all comparisons; therefore it is very time-consuming.
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At 69% where a â>â starts a new cluster a ââ at the end means that this sequence is the representative of this cluster a â%â is the identity between this sequence and the representative CD-HIT-2D CD-HIT-2D compares 2 protein datasets (db1, db2). For CD-HIT and CD-HIT-EST, users can upload a FASTA file, select a desired sequence identity level and other parameters.
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Default 0, perform psi-blast / pdb-blast type search -G (1/0) use global identity? Clicking this button opens a dialog where you can select the specific tables you want to document, as well as add extended properties to tables and columns.
The sequential number after the hyphen is not part of the tracking number. Don’t use -G 0 unless you use alignment coverage controls see options -aL, -AL, -aS, -AS -b band_width of alignment, default 20 -M max available memory (Mbyte), default 400 -n word_length, default 5, see user’s guide for choosing it -l length of throw_away_sequences, default 10 -t tolerance for redundance, default 2 -d length of description in .Clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space -s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster -S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60 -aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence -uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence -U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases -B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use -B 1 for huge databases -p 1 or 0, default 0 if set to 1, print alignment overlap in .Clstr file -T number of threads, default 1; with 0, all CPUs will be used -g 1 or 0, default 0 By cd-hit’s default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast mode).
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