PEP: Predictions for Entire Proteomes

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An explanation of the fields you can query through SRS in PEP, CHOP and CLUP:

PEP
Annotation	This is the original annotation from the genome sequencing project (the Description field is identical to the Annotation field in PEP).
MolWeight	Molecular weight of the sequence in Da.
OrganismClassification	The organism the protein came from is either classified as Prokaryote, Eukaryote, Virus or Archean.
EuclidFunction	Functional classification as assigned by Euclid. E.g. biosynthesis&cofactors will find all PEP entries that are predicted to synthesize cofactors.
PsiBlastNumAlignments	The number of alignments found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. This field will query the total number of alignments found against the three databases for each protein from PEP. E.g. 20:30 will find all proteins in PEP which had 20-30 homologs in the three databases.
PsiBlastHomologDBName	The databases homologs were found in, using PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. The three values you can search on are trembl, swissprot, and pdb. E.g. !pdb will exclude any proteins that aligned against PDB.
PsiBlastHomologID	The ID's of homologs which were found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB.
PsiBlastHomologSwissID	The ID's for homologs from SWISS-PROT which were found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB.
PsiBlastAlignmentLength	The alignment length of homologs found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. E.g. 45: will search for all PEP proteins that had an alignment greater than 45 residues in length.
PsiBlastPercentageIdentity	% identity of alignment when PSI-BLAST was used to align each protein against the public databases SWISS-PROT, TrEMBL and PDB. E.g 25:45 will search for all PEP proteins that had an alignment identity of 25% to 45%.
PsiBlastPercentageSimilarity	% similarity of alignment when PSI-BLAST was used to align each protein against the public databases SWISS-PROT, TrEMBL and PDB. E.g 25:45 will search for all PEP proteins that had an alignment similarity of 25% to 45%.
PsiBlastEValue	The 'e-value' of an alignment found by PSI-BLAST when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. The e-value is the probability of finding this alignment randomly. E.g. 0.001:0.003 will search for alignments where the probability of finding this alignment by chance is 1/1000 to 3/1000.
BlastPdbNumAlignments	The number of alignments found by PSI-BLAST when each protein was aligned against the public database PDB i.e. sequences with solved protein structures. This field will query the total number of alignments found against the three databases for each protein from PEP. E.g. 10:30 will find all proteins in PEP which had 10-30 homologs in PDB.
BlastPdbNumResiduesAligned	The total number of residues in a PEP sequence involved in alignments using PSI-BLAST when each protein was aligned against the public database PDB i.e. sequences with solved protein structures. E.g. 200:300 would find all PEP entries that had in total between 200 and 300 residues that were found to be part of homologs to be PDB entries (possibly consisting of multiple alignments that summate to this value).
BlastPdbRegionLength	The length of regions within a PEP sequence involved in alignments using PSI-BLAST when each protein was aligned against the public database PDB i.e. sequences with solved protein structures. E.g. 20:25 would find all PEP entries that had regions of 20-25 residues involved in aligments with PDB sequences.
CoiledCoilsNumRegions	The number of predicted coiled coil regions within a PEP entry. E.g. 3:5 will find all PEP entries that are predicted to have 3 to 5 coiled coils within their structure.
CoiledCoilsNumResidues	The total number of residues predicted to be part of coiled coils. E.g. 25:30 will find all PEP entries that are predicted to have 25-30 residues within coiled coil structures.
CoiledCoilRegionLength	The length of regions predicted to be part of coiled coils. E.g. 15:30 will find all PEP entries that are predicted to have a region of 15-30 residues within a coiled coil.
MaxHomNumAlignments	The number of hits found against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MaxHomHomologID	The ID's of hits found against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MaxHomPercentageIdentity	% identity of alignments against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MaxHomPercentageSimilarity	% similarity of alignments against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
NorsNumber	The number of non-regular secondary structure regions predicted within a PEP sequence. E.g. 3:5 will find all PEP sequences that are predicted to have 3-5 non-regular secondary structure regions.
NorsRegionLength	The length of predicted non-regular secondary structure regions.
ProfSecStructureAssignments	Secondary structure predicted by PHDsec. PHDsec assigns helicies as 'H', beta-sheets as 'E' and loops as 'L'. A typical PHDsec output would look like: HHHHHHHEEEEEELLLHHHHHEEEELLLEEEH' This sequence of letters represents the peptide in terms of how each base is predicted to constitute one of these secondary structure types. E.g. *HHHHHHHHHH* would find all PEP entries that are predicted to have a region of 10 bases making up a helix anywhere within their overall secondary stucture.
ProfNumHelicies	The number of helix regions predicted in a PEP sequence by PHDsec. E.g. 5: would find all PEP entries that are predicted to have over 5 regions that are alpha helicies.
ProfHelixRegionLength	The length of a helix region predicted in a PEP sequence by PHDsec. E.g. 10:15 would find all PEP entries that are predicted to have a region of 10-15 residues that is an alpha helix.
ProfNumBSheets	The number of beta-sheet regions predicted in a PEP sequence by PHDsec. E.g. 5: would find all PEP entries that are predicted to have over 5 regions that are beta sheets.
ProfBSheetRegionLength	The length of beta-sheet region predicted in a PEP sequence by PHDsec. E.g. 35: would find all PEP entries that are predicted to have a beta-sheet that is over 35 residues in length.
ProfNumLoops	The number of loop regions in a PEP sequence as predicted by PHDsec. E.g. 5: would find all PEP entries that are predicted to have at least 5 loop regions.
ProfLoopRegionLength	The length of a loop region in a PEP sequence as predicted by PHDsec. E.g. 105: would find all PEP entries that are predicted to have a loop region that is over 105 residues in length.
PhdHtmNumber	The number of transmembrane helicies in a PEP sequence as predicted by PHDhtm. E.g. 5: would find all PEP entries that are predicted to have over 5 transmembrane helicies within their overall structure.
PhdHtmNTerminalLocation	The n-terminal location if a transmembrane helix has been predicted by PHDhtm. The value is either intracellular or extracellular. E.g. intra* will find all PEP entries that are predicted to have a transmembrane helix with an intracellular n-terminal location.
PhdHtmRegionLength	The length of transmembrane helix region as predicted by PHDhtm. E.g. 100:120 will find all PEP entries that are predicted to have a transmembrane helix of between 100 and 120 residues in length.
SegNumResidues	The total number of residues expected to be part of low sequence complexity regions as predicted by SEG. E.g. 200:210 will find all PEP entries that are predicted to have between 200 and 210 residues found within low complexity regions.
SegRegionLength	The length of an individual low sequence complexity region as predicted by SEG. E.g. 100:150 will find all PEP entries that are predicted to have a low complexity region of 100 to 150 residues.
SignalPLen	The length of the predicted signal peptide. E.g. 1: will find all find all PEP entries that are predicted to have a signal peptide.
CHOP
PepID	The ID of the PEP protein the fragment was taken from.
ClusterID	The ID of the CLUP clusters that the fragment is found in.
Annotation	This is the original annotation from the genome sequencing project (the Description field is identical to the Annotation field in PEP).
MolWeight	Molecular weight of the sequence in Da.
OrganismClassification	The organism the protein came from is either classified as Prokaryote, Eukaryote, Virus or Archean.
EuclidFunction	Functional classification as assigned by Euclid. E.g. biosynthesis&cofactors will find all PEP entries that are predicted to synthesize cofactors.
PsiBlastNumAlignments	The number of alignments found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. This field will query the total number of alignments found against the three databases for each protein from PEP. E.g. 20:30 will find all proteins in PEP which had 20-30 homologs in the three databases.
PsiBlastHomologDBName	The databases homologs were found in, using PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. The three values you can search on are trembl, swissprot, and pdb. E.g. !pdb will exclude any proteins that aligned against PDB.
PsiBlastHomologID	The ID's of homologs which were found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB.
PsiBlastHomologSwissID	The ID's for homologs from SWISS-PROT which were found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB.
PsiBlastAlignmentLength	The alignment length of homologs found by PSI-BLAST, when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. E.g. 45: will search for all PEP proteins that had an alignment greater than 45 residues in length.
PsiBlastPercentageIdentity	% identity of alignment when PSI-BLAST was used to align each protein against the public databases SWISS-PROT, TrEMBL and PDB. E.g 25:45 will search for all PEP proteins that had an alignment identity of 25% to 45%.
PsiBlastPercentageSimilarity	% similarity of alignment when PSI-BLAST was used to align each protein against the public databases SWISS-PROT, TrEMBL and PDB. E.g 25:45 will search for all PEP proteins that had an alignment similarity of 25% to 45%.
PsiBlastEValue	The 'e-value' of an alignment found by PSI-BLAST when each protein was aligned against the public databases SWISS-PROT, TrEMBL and PDB. The e-value is the probability of finding this alignment randomly. E.g. 0.001:0.003 will search for alignments where the probability of finding this alignment by chance is 1/1000 to 3/1000.
BlastPdbNumAlignments	The number of alignments found by PSI-BLAST when each protein was aligned against the public database PDB i.e. sequences with solved protein structures. This field will query the total number of alignments found against the three databases for each protein from PEP. E.g. 10:30 will find all proteins in PEP which had 10-30 homologs in PDB.
BlastPdbNumResiduesAligned	The total number of residues in a PEP sequence involved in alignments using PSI-BLAST when each protein was aligned against the public database PDB i.e. sequences with solved protein structures. E.g. 200:300 would find all PEP entries that had in total between 200 and 300 residues that were found to be part of homologs to be PDB entries (possibly consisting of multiple alignments that summate to this value).
BlastPdbRegionLength	The length of regions within a PEP sequence involved in alignments using PSI-BLAST when each protein was aligned against the public database PDB i.e. sequences with solved protein structures. E.g. 20:25 would find all PEP entries that had regions of 20-25 residues involved in aligments with PDB sequences.
BlastFragmentsNumAlignments	The number of alignments found using PSI-BLAST, when each fragment was aligned against a database of all other fragments from CHOP.
BlastFragmentsHomologID	The ID of fragments found when aligning against all other fragments using PSI-BLAST. E.g. chopFrag54321 will find all fragments that were found to be homologous to the fragment chopFrag12345.
BlastFragmentsAlignmentLength	The length of alignments found when aligning against all other fragments using PSI-BLAST. E.g.200: will find all fragments that were also found to be homologous in a region of over 200 residues in length.
BlastFragmentsPercentageIdentity	The percentage identity of the alignment.
BlastFragmentsPercentageSimilarity	The percentage similarity of the alignment.
BlastFragmentsEValue	The 'e-value' of an alignment found by PSI-BLAST when each fragment was aligned against all other fragments. The e-value is the probability of finding this alignment randomly. E.g. 0.001:0.003 will search for alignments where the probability of finding this alignment by chance is 1/1000 to 3/1000.
CoiledCoilsNumRegions	The number of predicted coiled coil regions within a PEP entry. E.g. 3:5 will find all PEP entries that are predicted to have 3 to 5 coiled coils within their structure.
CoiledCoilsNumResidues	The total number of residues predicted to be part of coiled coils. E.g. 25:30 will find all PEP entries that are predicted to have 25-30 residues within coiled coil structures.
CoiledCoilRegionLength	The length of regions predicted to be part of coiled coils. E.g. 15:30 will find all PEP entries that are predicted to have a region of 15-30 residues within a coiled coil.
MaxHomNumAlignments	The number of hits found against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MaxHomHomologID	The ID's of hits found against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MaxHomPercentageIdentity	% identity of alignments against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MaxHomPercentageSimilarity	% similarity of alignments against SWISS-PROT when aligning PEP sequences using MaxHom. MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
ProfSecStructureAssignments	Secondary structure predicted by PHDsec. PHDsec assigns helicies as 'H', beta-sheets as 'E' and loops as 'L'. A typical PHDsec output would look like: HHHHHHHEEEEEELLLHHHHHEEEELLLEEEH This sequence of letters represents the peptide in terms of how each base is predicted to constitute one of these secondary structure types. E.g. *HHHHHHHHHH* would find all PEP entries that are predicted to have a region of 10 bases making up a helix anywhere within their overall secondary stucture.
ProfNumHelicies	The number of helix regions predicted in a PEP sequence by PHDsec. E.g. 5: would find all PEP entries that are predicted to have over 5 regions that are alpha helicies.
ProfHelixRegionLength	The length of a helix region predicted in a PEP sequence by PHDsec. E.g. 10:15 would find all PEP entries that are predicted to have a region of 10-15 residues that is an alpha helix.
ProfNumBSheets	The number of beta-sheet regions predicted in a PEP sequence by PHDsec. E.g. 5: would find all PEP entries that are predicted to have over 5 regions that are beta sheets.
ProfBSheetRegionLength	The length of beta-sheet region predicted in a PEP sequence by PHDsec. E.g. 35: would find all PEP entries that are predicted to have a beta-sheet that is over 35 residues in length.
ProfNumLoops	The number of loop regions in a PEP sequence as predicted by PHDsec. E.g. 5: would find all PEP entries that are predicted to have at least 5 loop regions.
ProfLoopRegionLength	The length of a loop region in a PEP sequence as predicted by PHDsec. E.g. 105: would find all PEP entries that are predicted to have a loop region that is over 105 residues in length.
PhdHtmNumber	The number of transmembrane helicies in a PEP sequence as predicted by PHDhtm. E.g. 5: would find all PEP entries that are predicted to have over 5 transmembrane helicies within their overall structure.
PhdHtmNTerminalLocation	The n-terminal location if a transmembrane helix has been predicted by PHDhtm. The value is either intracellular or extracellular. E.g. intra* will find all PEP entries that are predicted to have a transmembrane helix with an intracellular n-terminal location.
PhdHtmRegionLength	The length of transmembrane helix region as predicted by PHDhtm. E.g. 100:120 will find all PEP entries that are predicted to have a transmembrane helix of between 100 and 120 residues in length.
SegNumResidues	The total number of residues expected to be part of low sequence complexity regions as predicted by SEG. E.g. 200:210 will find all PEP entries that are predicted to have between 200 and 210 residues found within low complexity regions.
SegRegionLength	The length of an individual low sequence complexity region as predicted by SEG. E.g. 100:150 will find all PEP entries that are predicted to have a low complexity region of 100 to 150 residues.
SignalPLen	The length of the predicted signal peptide. E.g. 1: will find all find all PEP entries that are predicted to have a signal peptide.
CLUP
NumSequences	The number of sequences in the cluster found by PSI-BLAST, during an all versus all comparison of all fragements from CHOP. E.g. 10:20 will find all clusters in CLUP which had 10-20 sequences in the cluster.
SeedID	Searching on this field will find a cluster that has the fragment which matches your query as its seed.
SeedOrg	The organism the seed sequence came from.
SeedParentID	The parent ID, is the protein that the fragment used as the seed came from.
SeedLength	The length of the seed fragment.
SeedHitLength	The length of the alignment region in the seed fragment. E.g. 120: will find all clusters in CLUP that had an alignment between the seed and a sequence in the cluster that was over 120 residues on the seed sequence.
HomologID	The ID of a homolog which is part of the cluster found by PSI-BLAST, during an all versus all comparison of all fragements from CHOP. E.g. chopFrag12345 will find all clusters that have the sequence chopFrag12345 as a homolog within their cluster.
HomologOrg	The organism the homolog sequence came from. E.g. arath will find all clusters that have a.thaliana sequences as homologs in the cluster.
HomologParentID	The parent ID, is the protein that the homolog fragment came from.
HomologLength	The length of a homolog fragment.
HomologPercentageIdentity	% identity of an alignment found by PSI-BLAST during an all versus all comparison of all fragements from CHOP. E.g. 40: will find all clusters in CLUP which had an alignment of over 40% identity in the cluster.
HomologEValue	The 'e-value' of an alignment found by PSI-BLAST during an all versus all comparison of all fragements from CHOP. The e-value is the probability of finding this alignment randomly. E.g. 0.001:0.003 will search for alignments where the probability of finding this alignment by chance is 1/1000 to 3/1000.
HomologHitLength	The length of the alignment region in the homolog fragment. E.g. 200:250 will find all clusters in CLUP that had an alignment region on a homolog in the cluster that was between 200 and 250 residues in length.

PEP CUBIC