M.S.Gelfand Institute of Protein Research Russia Academy of Sciences Pushchino, Moscow Region, 142292 Russia phone: 7-(095)-135-11-41, 7-(095)-938-82-19 fax: 7-(095)-135-99-84 e-mail: misha@imb.imb.ac.ru
The following areas are essentially covered:
The following areas are referenced extensively but not exhaustively:
There are also some references on:
The field name starts at position 1.
The field content is indented to position 4.
Multiple contents are separated by semicolons.
Each 'identifier' is unique and consists of 8 characters:
A compatibility with the SEQANALREF data bank identifiers (see ACKNOWLEDGEMENTS) was attempted but not always sustained, especially in relaively late references.
The 'keywords' field contains keyword(s) describing the content of the publication. The list of the keywords is given below. Keywords describe, when appropriate, field, approach, structures, processes, ferments and sites being analyzed, and organisms involved.
The 'comment' field contains the information about the language of the publication (if not English), 'In press' note and maybe other short notes.
Entries are listed in identifier alphanumerical order.
identifier GELM9201 authors Gelfand M.S. title Computer functional analysis of nucleotide sequences: problems and approaches location in: Mathematical methods of the analysis of biopolymer sequences (DIMACS vol.8) (S.G.Gindikin, ed) (AMS, Providence RI, 1992) 19-61 keywords reviews; DNA models; statistics; prediction; functional sites; protein-coding regions; biomolecular linguistics; periodicity //
Versions starting with 9.1 can be obtained from anonymous ftp site imb.imb.ac.ru (147.45.3.14), directory /Biblio, as the single compressed file fans-ref.zip).
Version 3.4 of the data bank can be obtained from the EMBL file server at the Internet e-mail address
The file should contain nothing but the file server commands, e.g.
HELP HELP REFLIST DIR REFLIST GET REFLIST:FANS_REF.DOC GET REFLIST:FANS_REF.DAT
Version 4.3 is being published in "Biotechnology Software" journal (vol. 8, nos. 5, 6 (1991); vol. 9 nos. 1, 2, 3, 4, 6 (1992), vol. 10 nos. 4, 6 (1993) etc.).
If the data bank is extensively used or incorporated into another data bank, an acknowledgement would be appreciated.
To become a registered user one must fill the following form and mail and/or e-mail it to M.S.Gelfand at the address above.
....................... cut here .......................................... ======================= REGISTRATION FORM ============================ FANS-REF (Release 9.2) 1. Name ______________________________________________________________ 2. Address ___________________________________________________________ ___________________________________________________________________ 3. E-mail ____________________________________________________________ 4. Fax _______________________________________________________________ 5. Phone _____________________________________________________________ 6. Field of research _________________________________________________ ___________________________________________________________________ ___________________________________________________________________ 7. Other fields of interest __________________________________________ ___________________________________________________________________ ___________________________________________________________________ 8. Which computer system do you use? _________________________________ 9. Suggestions for the data bank development _________________________ ___________________________________________________________________ ___________________________________________________________________ 10. Date ______________________________________________________________ ....................... cut here ...........................................
I thank F.G.Ball, R.D.Blake, M.Borodovsky, B.Demeler, J.W.Fickett, D.Graur, R.Hanai, I.Iida, M.A.Jimenez-Montano, A.Konopka, E.V.Koonin, S.V.Korolev, E.V.Korotkov, J.Kypr, A.Marin, S.Ohno, P.A.Pevzner, A.A.Ptitsyn, V.A.Ratner, J.Rice, I.B.Rogozin, P.R.Sibbald, D.W.Smith, Yu.A.Sprizhitsky, V.B.Streletz, S.Tavare, E.N.Trifonov, M.S.Waterman, B.S.Weir, S.H.White, who supplied me with reprints of their works relevant to the data bank.
This data bank is or has been partially supported by the Russian State Program "Human Genome" (grant 534), Russian Fund of Fundamental Research (grant 94-04-12330), Department of Energy, USA (grant DE-FG02-94ER61919.A000), National Institutes of Health, USA (grant HG00783) and International Science Foundation (grant MTWOOO).
acceptor site (splicing) Acinetobacter amino acid control Bacillus subtilis biomolecular linguistics branch point (splicing) Caernorabilis elegans (nematode) CAP receptor caulimovirus CCAAT box (in eukaryotic promoters) chloroplasts ciliates codon usage compilation (of functional sites) complexity consensus Corynebacteria coxsackievirus cucumovirus cytomegalovirus databases Dictyostelium discoideum (slime mold) DNA models DNA-protein interaction DNA representation DNA structure (three-dimensional or thermostability parameters) DNAse I donor site (splicing) Drosophila E.coli echinoderms enhancer (of transcription) Entamoeba Epstein-Barr virus exons eukaryotes evolution exon-intron structure f1 (phage) fd (phage) flatworm Fourier transform fractals frame shift site functional sites fungi G4 (phage) Gallus gallus genetic code genetic language glucocorticoid control (of transcritpion in eukaryotes) glucocorticoid receptor green algae group I introns gyrase heat shock control (of transcription) herpes simplex HIV (virus) Homo sapiens honeybee hormone response IKe (phage) information theory initiation site (translation) integration integration host factor introns invertebrates Ising model kinetoplastids Klebsiella pneumoniae Lactobacillus lambda (phage) lentivirus LexA binding site long-range correlations M13 (phage) mammals Marchantia polymorpha Markov chain methylation Micrococcus luteus mitochondria mouse MS2 (phage) multiple alignment mutations neural network Neurospora nick site Nicotiana tabacum noncoding regions NotI site nucleosomes operator origin (replication) p53 pattern recognition (prediction methods) periodicity (see also 'nucleosomes') phages phiX174 (phage) plants plasmids Plasmodium poliovirus polyadenylation polyomavirus prediction primates probability (theory) prokaryptes promoter (of transcription) protein-coding regions protein ICP4 protein Mut Pseudomonas rabbit rat recombination relaxase repetitive elements replication restrictase EcoRI restriction site retrovirus Rev responsive element review rhinovirus rice RNA polymerase II (eukaryotic) RNA secondary structure rodents Rous sarcoma virus Salmonella typhimurium sequencing Serratia marcences similarity search splicing statistics Streptococcus pneumoniae SV40 (virus) T4 (phage) T7 (phage) target site termination site (translation) terminator (of transcription) Tetrahymena tobacco tobamovirus topoisomerase I topoisomerase II Toxoplasma translation transcription tRNA tymovirus vaccinia virus vertebrates virus BK viruses Walsh transform weight matrix wheat Xenopus yeast Zea mays