Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: Seqrutinator: Non-Functional Homologue Sequence Scrutiny for the Generation of large Datatsets for Protein Superfamily Analysis BackgroundIn recent years protein protein bioinformatics has resulted in much improved algorithms for multiple sequence alignment (MSA) and phylogeny. Few attention has been paid to sequence selection whereas particularly recently published complete proteomes often have many sequences that are partial or derive from pseudogenes. Not only do these sequences add noise to the MSA, phylogeny and other downstream computational analyses, they actually also instigate many errors in the processing of the MSAs and therewith all other downstream analyses, including the phylogeny.

ObjectiveHere we aim to provide and test an objective, automated and flexible pipeline for the scrutiny of sequence sets from large, complex protein superfamilies, resulting in the classification of sequences into either functional or non-functional. The pipeline should identify few Swissprot sequences and result in an improved MSA.

ResultsSeqrutinator is a pipeline that consists of five modules written in Python that identify and remove sequences that are likely Non-Functional Homologues. Here we tested the pipeline in its default order using default settings using three complex, related plant superfamilies (BAHD, CYP and UGT) that act in specialized metabolism, using the complete proteome of 16 plant species as input and using Swissprot as a control. Only 3.4% of Swissprot sequences were identified as NFH. Most NFH sequences are partial but, interestingly, their removal results in much shorter MSAs with many more reliable columns. Few but significant sequences that instigate gaps are found. The three superfamilies furthermore show similar scrutiny patterns.

Conclusion and perspectiveSeqrutinator forms a consistent pipeline for sequence scrutiny that does result in sequence sets that generate high fidelity MSAs. Additional tests will be performed in order to further demonstrate Seqrutinators performance.
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The categories of this paper are: biophysics
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The categories of this paper are: cognition
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The categories of this paper are: pharmacology
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The categories of this paper are: cancer
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The categories of this paper are: education
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The categories of this paper are: genetics
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The categories of this paper are: synthetic
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The categories of this paper are: developmental
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The categories of this paper are: microbiology
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The categories of this paper are: animal
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The categories of this paper are: neuroscience
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The categories of this paper are: immunology
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The categories of this paper are: systems
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The categories of this paper are: epidemiology
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The categories of this paper are: plant
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The categories of this paper are: biology