SLiMSuite REST Server


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SLiMSuite Documentation

Please note that command documentation sometimes lags behind the latest module versions. Click on module names to check current documentation.

cmd: seqin

Option Type: [?]{docs:?} FASFILE FILE SEQFILE

Modules: extatic orcfinder prothunter rje_mirna rje_price rje_slimfungo scap snp_mapper rje_pattern_discovery rje_seqgen rje_seqplot rje_yeast seqforker sfmap2png gopher_V2 qslimfinder_V1.9 slimfinder_V4.9 slimprob_V1.4 rje_biogrid rje_genbank rje_hpc rje_iridis rje_markov rje_pam rje_seqlist rje_seq rje_slimcore rje_tm aphid budapest fiesta gablam gasp gfessa gopher haqesac multihaq picsi qslimfinder seqmapper slimfarmer slimfinder slimmutant slimprob slimsearch unifake


ModuleOptionDescriptionDefault
aphid seqin=FILE Sequence file containing hits (if pepnorm != count) None
budapest seqin=FILE Name of EST fasta file used for search None
extatic seqin=FASFILE cDNA input seqence file (*.cdna.fas). See docs for naming advice. ExTATIC.cdna.fas
fiesta seqin=FILE EST file to be processed None
gablam seqin=FILE Query dataset file infile.fas
gasp seqin=FILE Fasta/ClustalW/Phylip Format sequence file infile.fas
gfessa seqin=FILE File containing EST/cDNA data to search for tags within None
gopher seqin=FILE Fasta file of 'query' sequences for orthology discovery (over-rides uniprotid=LIST)
gopher_V2 seqin=FILE Fasta file of 'query' sequences for orthology discovery
haqesac [seqin=?]{docs:?} ?
multihaq seqin=FILE Input query sequences None
orcfinder seqin=FILE Sequence file to search None
picsi seqin=FILE File containing sequences hit during searches None
prothunter [seqin=?]{docs:?} ?
qslimfinder seqin=FILE Sequence file to search None
qslimfinder_V1.9 seqin=FILE Sequence file to search None
rje_biogrid seqin=FILE Sequence file containing protein sequences with appropriate Accession Numbers/IDs None
rje_genbank seqin=FILE Input Genbank file
rje_hpc seqin=FILE Input sequence file to farm out None
rje_iridis seqin=FILE Input sequence file to farm out None
rje_markov seqin=FILE File with input sequences None
rje_mirna seqin=FILE Main file for analysis, containing UTRs
rje_pam seqin=FILE Sequence file from which to calculate AA freq for scaling None
rje_pattern_discovery seqin=FILE Sequence File to search None
rje_price seqin=FILE Input sequence alignment in fasta format (over-rides batch=LIST) None
rje_seq seqin=FILE Loads sequences from FILE (fasta,phylip,aln,uniprot or fastacmd names from fasdb) None
rje_seqgen seqin=FILE Input sequence file to randomise None
rje_seqlist seqin=FILE Sequence input file name. None
rje_seqplot seqin=FILE File containing input sequences None
rje_slimcore seqin=FILE Sequence file to search. Over-rules batch mode (and uniprotid=LIST). None
rje_slimfungo seqin=FILE File of input sequences None
rje_tm seqin=FILE Sequence file for which predictions have been made None
rje_yeast seqin=FILE Input sequence file containing yeast sequences Proteins.fas
scap seqin=FILE File with input sequences for testing None
seqforker seqin=FILE Input sequence file None
seqmapper seqin=FILE File of sequences to be mapped None
sfmap2png seqin=FILE *.mapping.fas file to use as input data
slimfarmer seqin=FILE Input sequence file to farm out None
slimfinder seqin=SEQFILE Sequence file to search. Over-rules batch=FILE and uniprotid=LIST None
slimfinder_V4.9 seqin=FILE Sequence file to search None
slimmutant seqin=FILE Input file with protein sequences
slimprob seqin=SEQFILE Sequence file to search. Over-rules batch=FILE and uniprotid=LIST None
slimprob_V1.4 seqin=FILE Sequence file to search None
slimsearch seqin=FILE Sequence file to search None
snp_mapper seqin=FILE Input Genbank file
unifake seqin=FILE Input sequence file. See rje_seq documentation for filtering options. None

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.