CSAH server



Detect Charged Single α-Helices in protein sequences
Description	Example	CSAH Server	Download

Example

Usage

The usage of the server is straightforward: you can provide an input protein sequence either by pasting a plin or FASTA sequence into the text entry field or you can also upload a FASTA file. Please note that the server only processes single sequences. (To run CSAH predictions on multiple sequences, you might want to use the downloadable standalone version).

The human inner centromere protein INCENP is provided as an example for demonstrating the usage of the CSAH Server. For a discussion on performance, see the evaluation section.

The ouput shows the sequence with CSAHs highlighted in bold capitals and coloring of charged residues.

A summary table is provided showing the positions of CSAHs according to the consensus of scan4csah and ft_charge as well as the corresponding segments detected by the two methods.
Three downloadable files are provided:

A csv file with the predicted CSAH positions (example: INCE_HUMAN_csah.csv):

Consensus,scan4csah,ft_charge
543-574,536-600,543-574
654-685,654-782,652-685

A FASTA file containing the input sequence with the CSAH segments masked by 'x' (example: INCE_HUMAN_masked.fst):

>Q9NQS7, CSAH segments masked
MGTTAPGPIHLLELCDQKLMEFLCNMDNKDLVWLEEIQEEAERMFTREFSKEPELMPKTP
SQKNRRKKRRISYVQDENRDPIRRRLSRRKSRSSQLSSRRLRSKDSVEKLATVVGENGSV
LRRVTRAAAAAAAATMALAAPSSPTPESPTMLTKKPEDNHTQCQLVPVVEIGISERQNAE
QHVTQLMSTEPLPRTLSPTPASATAPTSQGIPTSDEESTPKKSKARILESITVSSLMATP
QDPKGQGVGTGRSASKLRIAQVSPGPRDSPAFPDSPWRERVLAPILPDNFSTPTGSRTDS
QSVRHSPIAPSSPSPQVLAQKYSLVAKQESVVRRASRRLAKKTAEEPAASGRIICHSYLE
RLLNVEVPQKVGSEQKEPPEEAEPVAAAEPEVPENNGNNSWPHNDTEIANSTPNPKPAAS
SPETPSAGQQEAKTDQADGPREPPQSARRKRSYKQAVSELDEEQHLEDEELQPPRSKTPS
SPCPASKVVRPLRTFLHTVQRNQMLMTPTSAPRSVMKSFIKRNTPLRMDPKCSFVEKERQ
RLxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxEERLRKVLQARERVEQMKEEKKKQIE
QKFAQIDEKTEKAKEERLAEEKAKKKAAAKKMEEVEARRKQEEEARRLRWLQQxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxEQREQERREQERREQERREQERREQERREQERQLA
EQERRREQERLQAERELQEREKALRLQKEQLQRELEEKKKKEEQQRLAERQLQEEQEKKA
KEAAGASKALNVTVDVQSPACTSYQMTPQGHRAPPKINPDNYGMDLNSDDSTDDEAHPRK
PIPTWARGTPLSQAIIHQYYHPPNLLELFGTILPLDLEDIFKKSKPRYHKRTSSAVWNSP
PLQGARVPSSLAYSLKKH

A FASTA file containing the sequence(s) of the predicted CSAH segments (example: INCE_HUMAN_csah.fst):
```
>Q9NQS7 543-574
ENLRRKEEAEQLRRQKVEEDKRRRLEEVKLKR
>Q9NQS7 654-685
EEEERRHQELLQKKKEEEQERLRKAAEAKRLA
```

Evaluation

The INCENP protein was recently shown experimentally to contain a long CSAH segment (see Samejima et al, JBC 290:21460). The segment identified in thsi study spans residues 503-715. Note that, as demonstrated above, CSAHserver predicts two segments, 543-574 and 654-685 to from CSAHs. Thus, while it identifies the presence of CSAHs correctly, it does not find the entire segment by default. CSAHserver was designed to minimize the number of false positive hits and this usually comes at the price of missing some CSAHs. However, invoking CSAHserver with the method SCAN4CSAH only, the prediction obtained matches the experimental findings better: