PASV Output

pasv programs output a tab-separated text file (TSV) that lists key residues, signatures, and region of interest spanning info for each query sequence.

Here is how that file might look.

name pos_50 pos_52 pos_54 signature spans_start spans_end spans
AMK99662_spans_start_19_60_IQK I Q K IQK Yes No Start
AMK99662_spans_end_40_80_IQK I Q K IQK No Yes End
AMK99662_spans_start_20_60_IQK I Q K IQK Yes No Start
AMK99662_21_60_IQK I Q K IQK No No Neither
AMK99662_40_79_IQK I Q K IQK No No Neither
AMK99662_spans_end_40_81_IQK I Q K IQK No Yes End
AMK99662_spans_both_20_80_IQK I Q K IQK Yes Yes Both
AMK99662_spans_both_19_81_IQK I Q K IQK Yes Yes Both
AMK99662_21_79_IQK I Q K IQK No No Neither
AMK99662_full_length_IQK I Q K IQK Yes Yes Both
AMK99662_real_seq_IQK I Q K IQK Yes Yes Both
AMK99662_full_length_extra_IQK I Q K IQK Yes Yes Both
AMK99662_spans_start_20_60_ABC A B C ABC Yes No Start
AMK99662_spans_start_19_60_ABC A B C ABC Yes No Start
AMK99662_21_60_ABC A B C ABC No No Neither
AMK99662_spans_end_40_80_ABC A B C ABC No Yes End
AMK99662_spans_end_40_81_ABC A B C ABC No Yes End
AMK99662_40_79_ABC A B C ABC No No Neither
AMK99662_spans_both_20_80_ABC A B C ABC Yes Yes Both
AMK99662_spans_both_19_81_ABC A B C ABC Yes Yes Both
AMK99662_21_79_ABC A B C ABC No No Neither
AMK99662_full_length_ABC A B C ABC Yes Yes Both
AMK99662_real_seq_ABC A B C ABC Yes Yes Both
AMK99662_full_length_extra_ABC A B C ABC Yes Yes Both

Columns

  • name
    • The ID of the sequence.
    • I.e., the part of the fasta header up until the first space.
  • pos_50
    • This is the first key residue position.
    • It is the residue in the query that aligns with the residue in position 50 of the reference sequence.
  • pos_52
    • The 2nd key residue position
  • pos_54
    • The 3rd and final key residue position
  • signature
    • A concatenation of the residues at each of the key residue positions for each query sequence
  • spans_start
    • Does the query sequence span the start of a specified region of interest with numbering according to the key reference sequence?
    • Yes or No
  • spans_end
    • Does the query sequence span then end of a specified region of interest?
    • Yes or No
  • spans
    • Will be one of Neither, Start, End, or Both
    • Based on the values in spans_start and spans_end