Low Deep T - We Are One (2012).zip
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We are working on improving the automated data analysis pipeline to provide the predicted peptides and InterPro domains in addition to the transcripts and proteins, which can then be used to enhance the assemblies or for other functional analyses. We have already released a new version of the pipeline, which provides the predicted peptides and domains, as well as the Transdecoder-generated transcripts for these peptides, as a separate file. We plan to provide the following additional functionalities in future releases of the pipeline: (i) better handling of sequences with non-standard start/stop codons; (ii) better filtering of protein models obtained from translated sequences; (iii) better handling of sequences with partial CDS; (iv) better handling of sequences with no matches in NCBI nr, no matches in the Conserved Domain Database, or no matches in T. oceanica, and (v) better handling of sequences with hits to sequences from the Plant, Bacteria and Archaea Domains. We are also planning to release the pipeline in the format of a command-line application (with a Linux, UNIX or Windows executable) in order to enable additional functionalities, for example, performing a BLAST search for each gene or for all genes against a user-specified set of sequences, including the sequences of related species. All the data files and scripts we have created for our BLAST and protein analysis will be released as open source. We hope to be able to release all data generated by the pipeline in the future.
In addition to these publicly available files, we have also created a private GitHub repository, which includes all our data and scripts regarding the transcriptome assembly, functional annotation, and sequence analysis.
We are interested in learning more about all the datasets generated by your analysis and providing any feedback to help us improve the pipeline. Please let us know if you have any suggestions or comments, or if you would like to discuss any of the issues raised in this paper or in our paper describing the AUGUSTUS gene prediction software.
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Leaving Myers out, the rest of the group is worth considering. The Twins can offer Correa the money he wants to stay in the same division, and they can use him as a chip to try to land Myers, as well as the other players listed. Contreras is the only one with a realistic chance of reaching free agency. As for the other four, it's a crapshoot, but the Twins would have some leverage to receive a top prospect or young players. 827ec27edc