pip install flutileaadiff takes a multiple-sequence alignment as an input and creates a
character difference table. This command is designed for preparing amino acid
difference tables. Below is an example of a comparison of 4 H1 sequences.
flutile aadiff --subtype=H1 mufile.faa
| site | A02479030 | SD0246 | SD0272 | SD0136 |
|---|---|---|---|---|
| -3 | A | T | ||
| -2 | N | S | ||
| -1 | A | T | ||
| 1 | D | |||
| 154 | K | |||
| 154+1 | - | X | ||
| 154+2 | - | X | ||
| 155 | D | S | X | |
| 156 | D | G | N | X |
The --subtype=H1 argument tells flutile to align the inputs against an H1
reference (A/United Kingdom/1/1933). The reference is used to determine
relative indices (the sites column). The index reference is used only for
indexing and does not appear in the final table. The first three rows (sites
-3, -2, -1) align to the three residues at the end of the signal peptide. Site
1 is the first residue in the mature peptide. Any gaps in the reference
alignment are indexed as <ref_id>+<offset>, for example 154+1 and 154+2 are
positions 1 and 2 residues after the reference position 154.
flutile uses the references from (Burke 2014):
| HA | Reference | ||
|---|---|---|---|
| H1 | A/United Kingdom/1/1933 | MKARLLVLLCALAATDA | DTICIGYHANNS |
| H2 | A/Singapore/1/1957 | MAIIYLILLFTAVRG | DQICIGYHANNS |
| H3 | A/Aichi/2/1968 | MKTIIALSYIFCLPLG | QDLPGNDNSTATLCLGHHAVPN |
| H4 | A/swine/Ontario/01911–2/1999 | MLSIAILFLLIAEGSS | QNYTGNPVICLGHHAVSN |
| H5 | A/Vietnam/1203/2004 | MEKIVLLFAIVSLVKS | DQICIGYHANNS |
| H6 | A/chicken/Taiwan/0705/1999 | MIAIIVIATLAAAGKS | DKICIGYHANNS |
| H7 | A/Netherlands/219/2003 | MNTQILVFALVASIPTNA | DKICLGHHAVSN |
| H8 | A/turkey/Ontario/6118/1968 | MEKFIAIAMLLASTNA | YDRICIGYQSNNS |
| H9 | A/swine/Hong Kong/9/1998 | MEAASLITILLVVTASNA | DKICIGYQSTNS |
| H10 | A/mallard/bavaria/3/2006 | MYKIVVIIALLGAVKG | LDKICLGHHAVAN |
| H11 | A/duck/England/1/1956 | MEKTLLFAAIFLCVKA | DEICIGYLSNNS |
| H12 | A/duck/Alberta/60/1976 | MEKFIILSTVLAASFA | YDKICIGYQTNNS |
| H13 | A/gull/Maryland/704/1977 | MALNVIATLTLISVCVHA | DRICVGYLSTNS |
| H14 | A/mallard/Astrakhan/263/1982 | MIALILVALALSHTAYS | QITNGTTGNPIICLGHHAVEN |
| H15 | A/duck/Australia/341/1983 | MNTQIIVILVLGLSMVRS | DKICLGHHAVAN |
| H16 | A/black-headed-gull/Turkmenistan/13/1976 | MMIKVLYFLIIVLGRYSKA | DKICIGYLSNNS |
| H17 | A/little-yellow-shouldered bat/Guatemala/060/2010 | MELIILLILLNPYTFVLG | DRICIGYQANQN |
| H18 | A/flat-faced bat/Peru/033/2010 | MITILILVLPIVVG | DQICIGYHSNNS |
- The H3 signal peptide appears to actually be
MKTIIALSYIFCLALG
represent takes a multiple-sequence alignment as input and removes entries
that are similar in sequence and time. The function requires that headers have
a date term (with format year/month/day). For example:
>A|1990-01-02
GATACA
>B|1990-02-02
CATATA
There may be gaps in the alignment. Sequences in the alignment that are
separated by less than or equal to --max-day-sep and that are a sequence
identity of greather than or equal to --min-pident-sep will be clustered
together. A single representative is sampled from each cluster (the latest one
with ties resolved by order).
Extract the HA1 regions from (currently) H1 and H3 HA proteins.
- Burke, Smith (2014) A Recommended Numbering Scheme for Influenza A HA Subtypes