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Sequence set. DECODER, ORFfinder, Repeat Masker. Check ORF and for repeats in ORF. DDS, Clustal W. Clustering for non-redundant sequence set. Motif Discovery. BLASTP+SEG, E=0.1 complete linkage clustering. Find homologous sequences. Maximum density subgraph BLOSUM 50
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Sequence set DECODER, ORFfinder, Repeat Masker Check ORF and for repeats in ORF DDS, Clustal W Clustering for non-redundant sequence set Motif Discovery BLASTP+SEG, E=0.1 complete linkage clustering Find homologous sequences Maximum density subgraph BLOSUM 50 > 20 aa ungapped pairwise alignment Find conserved homologous regions Remove regions matching to known motifs HMMER Pfam BLASTP ProDom InterProScan InterPro and other motif databases New motif candidates Visual inspection of motif candidates Re-check predicted reading frames if necessary Motif Exploration Motif expansion by HMMER search of SwissProt/TrEMBL Multiple sequence alignment Secondary structure analysis Cellular localization Chromsomal localization Literature search, Interpretation of results Update control of other public motif database Re-filtering of motif candidates Reconcile motifs with newly reported motifs
0610039A16 D6Wsu147e[var](MMU) 2810011M06 ING1A[p33](HSA) LOC51147(HSA) ING1L(HSA) Similar to 1700027H23Rik(MMU) ING2(MMU) ING2(HSA) Similar to 1810018M11Rik(MMU) ING1(HSA) 2310010G05 D6Wsu147e(MMU) ING1[fragment 1](HSA) 1810018M11 1810018M11Rik(MMU) ING1C[p24](HSA) 1700027H23 1700027H23Rik(MMU) ING1C(HSA) my036(HSA) ING1[isoform1](MMU) 14013(ATHA) CG9293(DEML) ING1B[p24](HSA) YNL097C(SCER) ING1[p33](HSA) YHR090C(SCER) ING1[p47](HSA) SPAC3G9.08(S.pombe) ING1B[p33](HSA) ING3(HSA) ING1A[p47](HSA) ING3(MMU) ING1[fragment 2](HSA) ING3[p47 variant 2](HSA) CG7379(DEML) ING3[p47 variant 1](HSA) CG6632(DEML) 130013A07 130013A07Rik(MMU) DKFZP586C1218(HSA)