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The query for the search is one or several protein sequences, which are entered plain or in FASTA format.
Interestingly, we also detected several protein sequences in the studied group that were lineage-specific, and we presumed that these represented new genes or novel genes.
If several protein sequences were collected for a single gene; i.e., for genes with multiple alternatively spliced isoforms, then any duplicate sequences were discarded.
After a genome file is selected, one or several protein sequences are provided by the user, and the parameters for BLAT and Scipio are collected.
The analysis of the R. sanguineus sialotranscriptome revealed several protein sequences containing domains associated with protease inhibitors, such as Kunitz [ 56], thyropin [ 57, 58] and cystatins [ 59], as well as unique tick protease inhibitor domains, such as a tick carboxypeptidase inhibitor [ 60], and a tick anti-thrombin of the madanin/hirudin like family [ 61].
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If there were several protein sequencing companies out there, and you were a fairly established company and were making yourself popular with customers because you were the fastest, or you had the easiest to read results, you would want your ads to explain the benefits of your product.
Guided by several protein sequence analysis cases we have developed a dedicated tool that facilitates the visual comparison of different features related to the architecture of proteins.
The annotation of contigs has been proceeded using miR target prediction by MIRANDA, and protein function by similarity with several protein sequence databases by BLAST.
This method predicts the putative function for the protein from its sequence integrating the results from the PSI-BLAST programme and a fuzzy logic algorithm using several protein sequence characteristics which have been checked, with regards to their ability to rearrange a PSI-BLAST profile according more to their biological functions.
BLASTP search with M.PabI as a query led to the identification of several homologous protein sequences that are not associated with R.PabI homologs (data not shown).
Several ADH protein sequences from both Xenopus species were gathered at UniProt [ 28], first by name search and then by exploring clusters with 90% or 50% identity.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com