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Functional sequences were predicted for multiple perA gene copies through translation of each gene sequence using ExPASy online DNA sequence translation tool [ 32].
For the putative PCWDEs, the transcript sequences from the phasmids were converted to amino acid sequences using the ExPASy online translation tool [ 51].
In the second method the cDNA sequence was translated to protein sequence (ExPASy-translate tool, SIB; Swiss Institute of Bioinformatics) and then homologous proteins were searched using FASTA/SSEARCH/GGSEARCH/RCH - Protein Similarity Search (EMBL-EBI).
Predicted amino acid sequences were generated using the DNA sequence translate tools EXPASY http://www.expasy.ch/tools/dna.html.html
The amino acid sequence were deduced from the corresponding cDNA sequences using the translation tool at the ExPASy Proteomics website (http://expasy.org/tools/dna.html).html
Amino acid sequences were deduced from the corresponding cDNA sequences using the translation tool at the ExPASy Proteomics website (http://expasy.org/tools/dna.html).html
In silico translation (Expasy, translate tool [ 46]) and gene structure prediction (GENSCAN Web Server http://genes.mit.edu/GENSCAN.html, [ 47]) were performed on the opsin-like sequences retrieved from the draft genome of A. filiformis.
The DNA sequences provided by Beckman Coulter Genomics were converted into peptidic sequences with ExPASy Translate Tool (http://web.expasy.org).org
Nucleotide sequence from the whole genome of Geobacillus sp. strain WSUCF1 [ 15] was translated to amino acid sequence using ExPASy-Translate tool (http://web.expasy.org/translate/).org/translate/
The obtained nucleotide sequences were converted to protein sequences using the ExPASy Translate tool [ 49] and aligned using MUSCLE [ 50].
Transcript sequences were translated into the corresponding SPF precursor protein sequences with the ExPASy Translate tool [ 34].
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