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
orNo
spans_end
- Does the query sequence span then end of a specified region of interest?
Yes
orNo
spans
- Will be one of
Neither
,Start
,End
, orBoth
- Based on the values in
spans_start
andspans_end
- Will be one of