neurosnap.sequence package

Sequence analysis and utility modules.

Submodules

• neurosnap.sequence.align module
  • align_mafft()
  • alignment_coverage()
  • consensus_sequence()
  • pad_seqs()
  • read_msa()
  • run_mmseqs2()
  • run_mmseqs2_modes()
  • run_phmmer()
  • run_phmmer_mafft()
  • seqid()
  • write_msa()
• neurosnap.sequence.nucleotide module
  • generate_random_rna_sequence()
  • get_reverse_complement()
  • split_interleaved_fastq()
• neurosnap.sequence.protein module
  • aliphatic_index()
  • isoelectric_point()
  • molecular_weight()
  • net_charge()
  • sanitize_aa_seq()
• neurosnap.sequence.pssm module
  • PSSM
    • PSSM.background
    • PSSM.consensus
    • PSSM.counts
    • PSSM.msa_columns
    • PSSM.probabilities
    • PSSM.query
    • PSSM.query_positions
    • PSSM.scores
    • PSSM.sequence_weights
    • PSSM.to_dataframe()
  • ProfileAlignment
    • ProfileAlignment.aligned_a
    • ProfileAlignment.aligned_b
    • ProfileAlignment.end_a
    • ProfileAlignment.end_b
    • ProfileAlignment.mode
    • ProfileAlignment.pairs
    • ProfileAlignment.score
    • ProfileAlignment.start_a
    • ProfileAlignment.start_b
  • align_pssms()
  • align_sequence_to_pssm()
  • generate_pssm()
  • pssm_from_msa()
  • scan_sequence()
  • score_sequence()