HOW file format

The HOW file format (or just HOW file).

Secondary structure format (DSSP)

The secondary structure format uses the DSSP assignment:

G - 3-10 helix
I - pi-helix
H - alpha-helix
E - extended beta-sheet
B - beta-bridge
S - bend
L - other/loop

Note: Prediction servers typically use just three categories H, E, and L, where L is the rest. Sometimes H, G, and I are merged to H and sometimes E and B are merged to E, and L means the rest just as for the PredictProtein server.

Example HOW file

   178 1cdy.-
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKSPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSD      80
TYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT     160
VLQNQKKVEFKIDIVVLA
.EEEEEETTS.EEE..B..SSSS..EEEEETTS.EEEEEETTEEEE.S.TTGGGEE..GGGGGGTB..EEE.S..GGG.E      80
EEEEEETTEEEEEEEEEEEEEE.S.SEEETT..EEEEEE..TT....B..B.TTS.B..BSSEEEESS..STT.EEEEEE     160
EEETTEEEEEEEEEEEE.
   405 1phb.-
NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIP      80
REAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGL     160
PEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGG     240
LDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDE     320
RENACPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPA     400
TTKAV
......TTS.GGGB....TTS.TTGGG.HHHHHGGGGSTTS.SEEEE.GGG.EEEE.SHHHHHHHHH.TTTEETTS.SSS      80
HHHHHH...TTTT..TTTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHGGGSEEEHHHHTTTHHHHHHHHHHHT.     160
.GGGHHHHHHHHHHHHS..SSS.HHHHHHHHHHHHHHHHHHHHHS..SSHHHHHHT.EETTEE..HHHHHHHHHHHHHHH     240
HHHHHHHHHHHHHHHHH.HHHHHHHHH.GGGHHHHHHHHHHHT..B..EEEESS.EEETTEEE.TT.EEE..GGGTTT.T     320
TTSSSTTS..TT.S.....TT..GGG..TTHHHHHHHHHHHHHHHHHH....EE.TT....EE.SSB.EES..EEE..GG     400
G....
   344 1hle.A
MEQLSTANTHFAVDLFRALNESDPTGNIFISPLSISSALAMIFLGTRGNTAAQVSKALYFDTVEDIHSRFQSLNADINKP      80
GAPYILKLANRLYGEKTYNFLADFLASTQKMYGAELASVDFQQAPEDARKEINEWVKGQTEGKIPELLVKGMVDNMTKLV     160
LVNAIYFKGNWQQKFMKEATRDAPFRLNKKDTKTVKMMYQKKKFPYNYIEDLKCRVLELPYQGKELSMIILLPDDIEDES     240
TGLEKIEKQLTLDKLREWTKPENLYLAEVNVHLPRFKLEESYDLTSHLARLGVQDLFNRGKADLSGMSGARDLFVSKIIH     320
KSFVDLNEEGTEAAAATAGTILLA
.HHHHHHHHHHHHHHHHHHHHH.SSS.EEE.HHHHHHHHHHHHHT..HHHHHHHHHHHTGGGSTTHHHHHHHHHHHHT.S      80
S.SSEEEEEEEEEEETT....HHHHHHHHHHH..EEEEE.TTT.HHHHHHHHHHHHHHHTTTSSS.SS.TTSS.TTEEEE     160
EEEEEEEEEEBSS...GGG.EEEEEESSSS.EEEEEEEEEEEEEEEEEEGGGTEEEEEEEBTTSSEEEEEEEESS..SSS     240
SS.HHHHHT..HHHHHHHH.GGG.EEEEEEEEEE.EEEEEEEE.HHHHHHHT..GGG.TTT...HHHHSSS.EEEEEEEE     320
EEEEEE.SSEEEEEEEEEEEEEE.

Note: In the "old style" HOW format for output, the sequence length will occupy the first five positions of the header line, right adjusted. The new HOW format reserves the first six positions for the sequence length.

External links

• WebLogo — a web based application designed to make the generation of sequence logos as easy and painless as possible.
• plogo — Protein Sequence Logos using Relative Entropy
• RNA Structure Logo
• PredictProtein
• A Gallery of Sequence Logos
• Visualizing DNA binding sites: Sequence Logos and Walkers
• How Can I Make Sequence Logos on My Own Computer?
• STRING — Search Tool for the Retrieval of Interacting Proteins