*  Protein function prediction - Wikipedia
Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of ... coli protein sequences for homology in other genomes and find over 6000 pairs of sequences with shared homology to single ... 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Nature. 50 (5): 667. doi:10.1016/ ... Because the two sequences in each protein pair are non-homologous, these interactions could not be predicted using homology- ...
  https://en.wikipedia.org/wiki/Protein_function_prediction
*  Sequence homology - Wikipedia
January 2008). "TreeFam: 2008 Update". Nucleic Acids Research. 36 (Database issue): D735-40. doi:10.1093/nar/gkm1005. PMC ... Sequence homology is the biological homology between protein or DNA sequences, defined in terms of shared ancestry in the ... Homologous sequence regions are also called conserved. This is not to be confused with conservation in amino acid sequences, ... Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. The term "percent homology ...
  https://en.wikipedia.org/wiki/Sequence_homology
*  List of MeSH codes (G13) - Wikipedia
... sequence homology, amino acid MeSH G13.810.550 --- sequence homology, nucleic acid MeSH G13.810.550.830 --- synteny MeSH ... sequence deletion MeSH G13.920.590.762.180 --- chromosome deletion MeSH G13.920.590.762.320 --- gene deletion MeSH G13.920. ...
  https://en.wikipedia.org/wiki/List_of_MeSH_codes_(G13)
*  RAP2B - Wikipedia
... "cDNA sequence of a new ras-related gene (rap2b) isolated from human platelets with sequence homology to rap2". Nucleic Acids ... The most striking difference between the RAP and RAS proteins resides in their 61st amino acid: glutamine in RAS is replaced by ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... The proteins encoded by these genes share approximately 50% amino acid identity with the classical RAS proteins and have ...
  https://en.wikipedia.org/wiki/RAP2B
*  ORM1 - Wikipedia
... sequence homology with other human acute phase protein genes". Nucleic Acids Res. 13 (11): 3941-52. doi:10.1093/nar/13.11.3941 ... 1973). "Structure of 1 -acid glycoprotein. The complete amino acid sequence, multiple amino acid substitutions, and homology ... acid glycoprotein and the elucidation of the amino acid sequence of the carboxyl-terminal cyanogen bromide fragment". ... Board PG, Jones IM, Bentley AK (1986). "Molecular cloning and nucleotide sequence of human alpha 1 acid glycoprotein cDNA". ...
  https://en.wikipedia.org/wiki/ORM1
*  List of MeSH codes (G06) - Wikipedia
... amino acid MeSH G06.184.842.200.820 --- structural homology, protein MeSH G06.184.842.550 --- sequence homology, nucleic acid ... repetitive sequences, nucleic acid MeSH G06.184.603.080.708.330 --- interspersed repetitive sequences MeSH G06.184.603.080. ... src homology domains MeSH G06.184.603.790.709.805 --- structural homology, protein MeSH G06.184.842.200 --- sequence homology, ... regulatory sequences, nucleic acid MeSH G06.184.603.080.689.330 --- enhancer elements (genetics) MeSH G06.184.603.080.689.330. ...
  https://en.wikipedia.org/wiki/List_of_MeSH_codes_(G06)
*  Hemopexin - Wikipedia
"The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology". Nucleic Acids ... "The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology". Nucleic Acids ... As the introns were not placed randomly; they fell in the center of the region of amino acid sequence homology in strikingly ... Computer-assisted analysis of the internal homology in amino acid sequence suggested duplication of an ancestral gene thus ...
  https://en.wikipedia.org/wiki/Hemopexin
*  CS-BLAST - Wikipedia
"The MPI Bioinformatics Toolkit as an Integrative Platform for Advanced Protein Sequence and Structure Analysis." Nucleic Acids ... Homology is the relationship between biological structures or sequences derived from a common ancestor. Homologous proteins ( ... Nucleic Acids Research 25.17 (1997): 3389-402. Oxford University Press. Print [4] Bigert, A., and J. Söding. "Sequence Context- ... The figure illustrates the sequence to sequence and profile to sequence equivalence with the alignment matrix. The query ...
  https://en.wikipedia.org/wiki/CS-BLAST
*  Transcription factor II E - Wikipedia
"Identification of two large subdomains in TFIIE-alpha on the basis of homology between Xenopus and human sequences". Nucleic ... Acids Res. 20 (21): 5838. doi:10.1093/nar/20.21.5838. PMC 334425 . PMID 1454543. Heng HH, Xiao H, Shi XM, Greenblatt J, Tsui LC ... Sumimoto H, Ohkuma Y, Sinn E, Kato H, Shimasaki S, Horikoshi M, Roeder RG (1991). "Conserved sequence motifs in the small ... "Structural motifs and potential sigma homologies in the large subunit of human general transcription factor TFIIE". Nature. 354 ...
  https://en.wikipedia.org/wiki/Transcription_factor_II_E
*  Cadang-cadang - Wikipedia
Coconuts from Asia and South Pacific have been found to have viroids with similar nucleic acid sequences of CCCVd. The ... Moreover, they share sequence homology with other viroids. Conditions for a viroid to infect its host include wounds on the ... The first step is the purification to obtain the nucleic acids of the plant cells. The leaves of the plant located four or more ... This viroid has 64% sequence homology with the cadang-cadang viroid. There are other related viroids with the CCCVd, which are ...
  https://en.wikipedia.org/wiki/Cadang-cadang
*  T-Coffee - Wikipedia
... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... Nucleic Acids Res. 39 (Web Server issue): W13-7. doi:10.1093/nar/gkr245. PMC 3125728 . PMID 21558174. Kemena C, Notredame C ( ... In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can ... It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences ...
  https://en.wikipedia.org/wiki/T-Coffee
*  DDX5 - Wikipedia
Hloch P, Schiedner G, Stahl H (1990). "Complete cDNA sequence of the human p68 protein". Nucleic Acids Res. 18 (10): 3045. doi: ... Ford MJ, Anton IA, Lane DP (1988). "Nuclear protein with sequence homology to translation initiation factor eIF-4A". Nature. ... 2000). "Structure and expression of the human p68 RNA helicase gene". Nucleic Acids Res. 28 (4): 932-9. doi:10.1093/nar/28.4. ... Nucleic Acids Res. 31 (5): 1470-80. doi:10.1093/nar/gkg236. PMC 149829 . PMID 12595555. Wilson BJ, Giguère V (2007). " ...
  https://en.wikipedia.org/wiki/DDX5
*  Loop modeling - Wikipedia
The problem arises often in homology modeling, where the tertiary structure of an amino acid sequence is predicted based on a ... The FALC-Loop web server for protein loop modeling" Nucleic Acids Research 39, W210-W214 (2011). Lee J, Lee D, Park H, Coutsias ... Chung SY, Subbiah S. (1996.) A structural explanation for the twilight zone of protein sequence homology" Structure 4: 1123-27 ... The extent of the inaccuracy increases with the number of amino acids in the loop. The loop amino acids' side chains dihedral ...
  https://en.wikipedia.org/wiki/Loop_modeling
*  PDGFB - Wikipedia
"Nucleotide sequence of transforming human c-sis cDNA clones with homology to platelet-derived growth factor". Nucleic Acids Res ...
  https://en.wikipedia.org/wiki/PDGFB
*  Epstein-Barr virus stable intronic-sequence RNAs - Wikipedia
This unstructured stretch of sequence may be exposed to allow for interactions with nucleic acids or other proteins. The sisRNA ... sequence is ~100% conserved in EBV strains and homology extends to include other lymphocryptoviruses. The hairpin structure is ... Nucleotides 4 to 26 of ebv-sisRNA-1 form a short hairpin loop that presents a Uridine-rich sequence motif (a possible platform ... Epstein-Barr virus stable intronic-sequence RNAs (ebv-sisRNAs) are a class of non-coding RNAs generated by repeat introns in ...
  https://en.wikipedia.org/wiki/Epstein%E2%80%93Barr_virus_stable_intronic-sequence_RNAs
*  WU polyomavirus - Wikipedia
WU virus was discovered by shotgun sequencing of the nucleic acids found in the respiratory secretions of a young patient ... Sequence homology was detected among the sequences found in the clinical sample and the known genomes of other human ... The complete genome of the WU virus has been sequenced and found to be a circular double-stranded DNA genome of 5229 base pairs ...
  https://en.wikipedia.org/wiki/WU_polyomavirus
*  Carbonic anhydrase II - Wikipedia
Venta PJ, Tashian RE (1990). "PCR detection of the TAQ1 polymorphism at the CA2 locus". Nucleic Acids Res. 18 (18): 5585. doi: ... 1988). "Cloning, expression, and sequence homologies of cDNA for human carbonic anhydrase II". Genomics. 1 (2): 159-66. doi: ... Nucleic Acids Res. 15 (11): 4687. doi:10.1093/nar/15.11.4687. PMC 340889 . PMID 3108857. Murakami H, Marelich GP, Grubb JH, et ... Montgomery JC, Venta PJ, Tashian RE, Hewett-Emmett D (1987). "Nucleotide sequence of human liver carbonic anhydrase II cDNA". ...
  https://en.wikipedia.org/wiki/Carbonic_anhydrase_II
*  Anders Krogh - Wikipedia
Krogh A, Mian IS, Haussler D (1994). "A hidden Markov model that finds genes in E. coli DNA". Nucleic Acids Res. 22 (22): 4768- ... 1996). "Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology". Comput. Appl. ... Nucleic Acids Res. 36 (Database issue): D102-6. doi:10.1093/nar/gkm955. PMC 2238834 . PMID 18006571. Lindow M, Jacobsen A, ... Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, doi:10.2277/ ...
  https://en.wikipedia.org/wiki/Anders_Krogh
*  List of restriction enzyme cutting sites: Bsa-Bso - Wikipedia
... which recognizes the novel hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3'". Nucleic Acids Res. 27 (13): 2644-5. doi:10.1093/nar/ ... Rina M, Markaki M, Bouriotis V (December 1994). "Sequence of the cloned bseCIM gene: M.BseCI reveals high homology to M.BanIII ... and the discovery of a wrongly sequenced site in pACYC177". Nucleic Acids Res. 19 (9): 2321-3. doi:10.1093/nar/19.9.2321. PMC ... which recognizes the pentanucleotide sequence 5'-CTCAG(N)(10/8)". Nucleic Acids Res. 29 (4): 895-903. doi:10.1093/nar/29.4.895 ...
  https://en.wikipedia.org/wiki/List_of_restriction_enzyme_cutting_sites:_Bsa%E2%80%93Bso
*  TOP2B - Wikipedia
... complete coding sequence and homology with other type II topoisomerases". Biochimica et Biophysica Acta. 1172 (3): 283-91. doi: ... Nucleic Acids Research. 21 (16): 3719-23. doi:10.1093/nar/21.16.3719. PMC 309874 . PMID 8396237. Nakano H, Yamazaki T, Miyatake ... Nucleic Acids Research. 20 (21): 5587-92. doi:10.1093/nar/20.21.5587. PMC 334390 . PMID 1333583. "Entrez Gene: TOP2B ... Ng SW, Liu Y, Schnipper LE (Dec 1997). "Cloning and characterization of the 5'-flanking sequence for the human DNA ...
  https://en.wikipedia.org/wiki/TOP2B
*  RNASE1 - Wikipedia
Beintema JJ, Wietzes P, Weickmann JL, Glitz DG (Jan 1984). "The amino acid sequence of human pancreatic ribonuclease". ... Nucleic Acids Research. 20 (3): 612. doi:10.1093/nar/20.3.612. PMC 310435 . PMID 1741299. Sakakibara R, Hashida K, Tominaga N, ... N-terminal sequence homology with human nonsecretory ribonuclease". Chemical & Pharmaceutical Bulletin. 39 (1): 146-9. doi: ... Haugg M, Schein CH (Feb 1992). "The DNA sequences of the human and hamster secretory ribonucleases determined with the ...
  https://en.wikipedia.org/wiki/RNASE1
*  Papillomaviridae - Wikipedia
E6 is a 151 amino-acid peptide that incorporates a type 1 motif with a consensus sequence -(T/S)-(X)-(V/I)-COOH. It also has ... Coggins LW, Ma JQ, Slater AA, Campo MS (1985). "Sequence homologies between bovine papillomavirus genomes mapped by a novel low ... Nucleic Acids Res. 20 (11): 2889. doi:10.1093/nar/20.11.2889. PMC 336941 . PMID 1319576. Varsani A1, Kraberger S, Jennings S, ... Compared to other papillomavirus genes, the amino acid sequences of most portions of L1 are well-conserved between types. ...
  https://en.wikipedia.org/wiki/Papillomaviridae
*  Multiple sequence alignment - Wikipedia
... probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998. Söding J (2005). "Protein homology ... Notredame C, O'Brien EA, Higgins DG (1997). "RAGA: RNA sequence alignment by genetic algorithm". Nucleic Acids Res. 25 (22): ... Edgar RC (2004). "MUSCLE: multiple sequence alignment with high accuracy and high throughput". Nucleic Acids Research. 32 (5): ... Notredame C, Higgins DG (1996). "SAGA: sequence alignment by genetic algorithm". Nucleic Acids Res. 24 (8): 1515-24. doi: ...
  https://en.wikipedia.org/wiki/Multiple_sequence_alignment
*  PyrD leader - Wikipedia
Nucleic Acids Research. 22 (4): 625-31. doi:10.1093/nar/22.4.625. PMC 307853 . PMID 7510398. Turnbough CL, Switzer RL (2008). " ... "The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology ... Translation initiation can occur at more than one different site within this leader sequence, under high CTP or GTP conditions ... This hairpin blocks ribosome-binding at the Shine-Dalgarno sequence, and therefore blocks expression of PyrD. Under low CTP/GTP ...
  https://en.wikipedia.org/wiki/PyrD_leader
*  List of sequence alignment software - Wikipedia
1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University ... Girdea, M; Noe, L; Kucherov, G (January 2010). "Back-translation for discovering distant protein homologies in the presence of ... Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: ... September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 ...
  https://en.wikipedia.org/wiki/List_of_sequence_alignment_software