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These traces were downloaded and searched against our dataset using the standalone BLAST package (TBLASTx and TBLASTn algorithms with default gap costs and the BLOSUM62 matrix).
Sequence traces were downloaded, imported into Contig Express model of the VectorNTI Advance 11 software (Invitrogen, Carlsbad, CA, USA), assembled and manually evaluated for polymorphisms.
About 16 million traces were downloaded from the NCBI Trace Archive [ 64] and translated, without prior masking, into the six possible reading frames, taking into account only those ORF sequences longer than at least 50 amino acids.
To identify putative GATA conserved domains, whole genome traces were downloaded to a local database and searched using two previously described Platynereis GATA factors and TblastN with each individual genome.
Human genome project (HGP) sequencing traces were downloaded from the NCBI Trace Archive (http://www.ncbi. nlm.nih.gov/Traces/) and aligned to the reference genome (build NCBI36/hg18, March 2006) using the GSAssembler V2 software (Roche, Burgess Hill, West Sussex, UK).
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The trace files were downloaded from NCBI Trace Archive.
P. sojae trace file sequences were downloaded from the NCBI Trace File Archive (www.ncbi.nlm.nih.gov).nih.gov
The traces identified by these searched were downloaded in.scr trace format for assembly into contigs.
Genomic sequence data was produced by the Washington University Genome Sequencing Center in St . Louis although trace sequences to generate the URFs database were downloaded from NCBI Trace server.
The traces identified by these searches were downloaded in.fasta format and cross checked to eliminate duplicate results.
Second, alignments of human genome resequencing data generated by the 1000 Genomes Project were downloaded (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/), and 100 individuals who represent subpopulations were arbitrarily selected.
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