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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].
Genomic and cDNA sequences were translated to amino acids using Expasy's Translate Tool; the corresponding reading frame was determined based on the presence of the reported sequences for KETc1 and KETc7.
The longest ORF from the conceptual translation (universal genetic code) of the ESTs of Psalteriomonas was obtained for each gene using Expasy's Translate tool http://www.expasy.org/tools/dna.html.html
Predicted amino acid sequences were generated using the DNA sequence translate tools EXPASY http://www.expasy.ch/tools/dna.html.html
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).
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
A The open reading frame of three complete sequences were analyzed using the translation tool of the ExPASy proteomics server (www.expasy.ch) from the Swiss Institute of Bioinformatics SIBB) [41] and the InterProScan Sequence Search of EBML-EBI.
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 protein sequence of Oryzias latipes Barhl2 was obtained from translating the sequenced cDNA clone using the ExPASy online translate tool from Swiss Institute of Bioinformatics SIBB).
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