flutile 0.13.3

sequence analysis tools for flu research

flutile

Installation

pip install flutile

Commands

aadiff

aadiff 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):

--- | ------------------------------------------------- | ------------------- | ---------------------- | 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

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).

trim

Extract the HA1 regions from (currently) H1 and H3 HA proteins.

References

1. Burke, Smith (2014) A Recommended Numbering Scheme for Influenza A HA Subtypes