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Bielefeld University Bioinformatic Service

PoSSuMsearch - Manual

This manual consists a short explanation of all parameters supported by the online version of the PoSSuM software package.. For a more detailed description, please refer to the manual: PDF or PS.

FASTA

A sequence in FASTA format is described as follows:

a sequence consists of one header line, followed by one or more data lines
a header line allways begins with a >
the first word after the > character is the sequence id , the rest of the line is the sequence description
the data lines contain the sequence data and should not longer than 80 characters
a FASTA file can contain more than one sequence

An example for a single sequence in FASTA format :

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY

Motif DB

One of prints37 or blocks14.2.

Search Algorithm

One of esa (enhanced suffix array algorithm), lahead (Look ahead search algorithm) or simple (Simple search algorithm).

Ouput Format

One of human, cisml or tabs.

type of input sequence

...

Output Restriction

eval: An E-value to determine the threshold from.
pval: A p-value to determine the threshold from.
mssth: A matrix similarity score (MSS) to determine the threshold from.
rawth: Raw threshold value.
best Search for k best matches for each PSSM.