Analysis of the Sargasso Sea Resource and Its Impact on Database Composition
Author Information
Author(s): Tress Michael L, Cozzetto Domenico, Tramontano Anna, Valencia Alfonso
Primary Institution: Protein Design Group, CNB-CSIC, Madrid, Spain
Hypothesis
How do the Sargasso Sea sequences influence the classification and analysis of known protein families?
Conclusion
The Sargasso Sea sequences introduce significant challenges for bioinformatics analyses due to their high proportion of sequence fragments.
Supporting Evidence
- The Sargasso Sea resource contains over one million distinct protein sequences from approximately 1,800 new species.
- Many sequences in the Sargasso Sea resource are fragments, leading to poor quality alignments.
- Only 11,700 sequences from the Sargasso Sea database overlap with existing databases at 90% identity.
Takeaway
The Sargasso Sea has a lot of new genetic information, but it's tricky to use because many of the sequences are just pieces of proteins.
Methodology
The study involved analyzing the Sargasso Sea sequences and comparing them with existing protein databases to assess their impact on sequence classification and alignment.
Potential Biases
The presence of many fragments may lead to biased conclusions about protein families and their distributions.
Limitations
The high proportion of sequence fragments in the Sargasso Sea resource complicates the analysis and interpretation of the data.
Digital Object Identifier (DOI)
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