Read assembly and protein disorder

OlcAssembly: overlap-layout-consensus assembly. Duplicate and contained reads are dropped, longest suffix-prefix overlaps (at most floor(max_error L) mismatches) are accepted greedily longest first without branching or cycles, and each contig is the column-majority consensus of its layout. ProteinDisorder: FoldIndex 2.785 H - abs(R) - 1.151 from rescaled Kyte-Doolittle hydropathy and net charge, globally and in a sliding window. Identical to the Python arm morie.fn.bioseqx (read indices and layouts 0-based there, 1-based here).

Usage

OlcAssembly(long_reads, min_overlap = 3L, max_error = 0)

ProteinDisorder(sequence, window = 51L, min_region = 5L)

Arguments

long_reads

Character vector of reads.

min_overlap

Minimum overlap length.

max_error

Maximum mismatch fraction inside an overlap.

sequence

Protein sequence (one-letter codes).

window

Odd sliding-window length.

min_region

Minimum length of a reported disordered region.

Value

List. OlcAssembly: contigs, layouts (matrices of read, offset), overlaps, n_reads_used. ProteinDisorder: fold_index, mean_hydropathy, mean_net_charge, profile, disordered, regions, fraction_disordered.

References

Myers, E. W. (2005). The fragment assembly string graph. Bioinformatics 21 (suppl. 2), ii79-ii85.

Prilusky, J. et al. (2005). FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21, 3435-3438.

Uversky, V. N., Gillespie, J. R. and Fink, A. L. (2000). Why are natively unfolded proteins unstructured under physiologic conditions? Proteins 41, 415-427.

Examples

OlcAssembly(c("ATGGCGT", "GCGTGCA", "TGCAATG", "CAATGGA"))$contigs
#> [1] "ATGGCGTGCAATGGA"
ProteinDisorder("MKKEEEKKPSEESKEDKKSEEGAPLLIVAVLLFAGIVLLVAWFILK", window = 11)$regions
#> [[1]]
#> [1]  1 21
#>