HOW file format - Revision history

Christoph: /* See also */

2007-06-24T03:07:03Z

‎See also

Christoph at 03:06, 24 June 2007

2007-06-24T03:06:45Z

Christoph: /* Secondary structure format (DSSP) */

2007-06-24T01:44:46Z

‎Secondary structure format (DSSP)

Christoph at 01:31, 24 June 2007

2007-06-24T01:31:49Z

Christoph: /* External links */

2007-06-15T21:55:03Z

‎External links

Christoph at 09:05, 9 June 2007

2007-06-09T09:05:30Z

Christoph: /* Secondary structure format (DSSP) */

2007-06-09T08:49:50Z

‎Secondary structure format (DSSP)

Christoph at 08:49, 9 June 2007

2007-06-09T08:49:13Z

Christoph at 08:19, 9 June 2007

2007-06-09T08:19:05Z

New page

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 [http://www.predictprotein.org/ PredictProtein server].''

==Example HOW file==
<pre>
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.
</pre>

''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==
*[http://www.cbs.dtu.dk/%7Egorodkin/appl/plogo.html plogo] — Protein Sequence Logos using Relative Entropy
*[http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html RNA Structure Logo]
*[http://www.predictprotein.org/ PredictProtein]
*[http://www.ccrnp.ncifcrf.gov/~toms/sequencelogo.html A Gallery of Sequence Logos]

[[Category:Bioinformatics]]

@@ Line 69: / Line 69: @@
 ==See also==
 *[[Tab file format]]
-*[[HOW file format]]
+*[[Column file format]]
 ==References==

← Older revision		Revision as of 03:06, 24 June 2007
Line 66:		Line 66:

	''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.''		''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.''
		+
		+	==See also==
		+	*[[Tab file format]]
		+	*[[HOW file format]]

	==References==		==References==

@@ Line 18: / Line 18: @@
 ==Secondary structure format (DSSP)==
-The secondary structure format uses the [[DSSP]] assignment<ref>(1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. ''Biopolymers, 22(12):2577-637. PMID: 6667333.''</ref>:
+The secondary structure format uses the [[DSSP]] assignment<ref name="Kabsch1983">Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". ''Biopolymers, 22(12):2577-2637. PMID: 6667333''.</ref>:
   G - 3-10 helix
   I - pi-helix

@@ Line 18: / Line 18: @@
 ==Secondary structure format (DSSP)==
-The secondary structure format uses the DSSP assignment:
+The secondary structure format uses the [[DSSP]] assignment<ref>(1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. ''Biopolymers, 22(12):2577-637. PMID: 6667333.''</ref>:
   G - 3-10 helix
   I - pi-helix
@@ Line 67: / Line 67: @@
 ''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==
 *[http://string.embl.de/ STRING] &mdash; Search Tool for the Retrieval of Interacting Proteins
 [[Category:Bioinformatics]]

@@ Line 1: / Line 1: @@
 The '''HOW file format''' (or just '''HOW file''').
 ==Secondary structure format (DSSP)==
@@ Line 10: / Line 26: @@
   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 [http://www.predictprotein.org/ PredictProtein server].''
@@ Line 15: / Line 32: @@
 ==Example HOW file==
 <pre>
 1cdy.-
 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKSPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSD      80
 TYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT     160
@@ Line 22: / Line 39: @@
 EEEEEETTEEEEEEEEEEEEEE.S.SEEETT..EEEEEE..TT....B..B.TTS.B..BSSEEEESS..STT.EEEEEE     160
 EEETTEEEEEEEEEEEE.
 1phb.-
 NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIP      80
 REAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGL     160
@@ Line 35: / Line 52: @@
 TTSSSTTS..TT.S.....TT..GGG..TTHHHHHHHHHHHHHHHHHH....EE.TT....EE.SSB.EES..EEE..GG     400
 G....
 1hle.A
 MEQLSTANTHFAVDLFRALNESDPTGNIFISPLSISSALAMIFLGTRGNTAAQVSKALYFDTVEDIHSRFQSLNADINKP      80
 GAPYILKLANRLYGEKTYNFLADFLASTQKMYGAELASVDFQQAPEDARKEINEWVKGQTEGKIPELLVKGMVDNMTKLV     160

@@ Line 3: / Line 3: @@
 ==Secondary structure format (DSSP)==
 The secondary structure format uses the DSSP assignment:
-  G	3-10 helix
+  G - 3-10 helix
-  I	pi-helix
+  I - pi-helix
-  H	alpha-helix
+  H - alpha-helix
-  E	extended beta-sheet
+  E - extended beta-sheet
-  B	beta-bridge
+  B - beta-bridge
-  S	bend
+  S - bend
-  L	other/loop
+  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 [http://www.predictprotein.org/ PredictProtein server].''

@@ Line 51: / Line 51: @@
 ==External links==
 *[http://www.cbs.dtu.dk/%7Egorodkin/appl/plogo.html plogo] &mdash; Protein Sequence Logos using Relative Entropy
 *[http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html RNA Structure Logo]
 *[http://www.predictprotein.org/ PredictProtein]
 *[http://www.ccrnp.ncifcrf.gov/~toms/sequencelogo.html A Gallery of Sequence Logos]
 [[Category:Bioinformatics]]