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Quick Search: User can search and retrieve information on sequences, patterns and consensus sequences for each of the proteins involved in blood coagulation pathway (BCPs).
Simple Search: User can search for specific entries using the appropriate combination of keywords.
A complete list of search fields and their description is given below:
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Protein Name |
User can search for protein name.
E.g. Thrombin
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Accession Number |
NCBI accession number can be used to search the database.
E.g. Q90244
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Source |
User can search either using genus, species or common name as keyword.
E.g. human
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Taxonomy |
The sequences are classified as Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
E.g. Homo sapien
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| Sequence length |
To search for sequences of a defined length.
E.g. 200 |
| Features |
This field allows user to search for biological features of the sequence.
E.g. disulfide |
Function |
User can search for particular function of BCPs.
E.g. coagulation
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Subcellular location |
User can search for subcellular location of the BCPs.
E.g. Secreted
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Subunit structure |
User can search for quaternary structure of BCPs.
E.g. Heterohexamer
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| Tissue specificty |
This field allows to search the discription of the expression of a gene in different tissues.
E.g. Plasma |
Disease |
Description of the disease(s) associated with the deficiency of BCPs.
E.g. Thrombophilia
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Post-translation modification |
Description of post-translation modifications of BCPs.
E.g. Sulfation
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Advanced Search: User can refine the search by using appropriate combinations of keywords and boolean operators.
All searches are case insensitive.
Mutations
User can retrieve information on all types of mutations viz., missense, nonsense, insertion, deletion, polymorphism and splice site mutations that are reported in literature for human BCPs. Information on the complete protein sequence, position of the mutation, the wild type and mutant residues, domain, codon, exon/intron involved and the relevant literature links are displayed in a tabular format for each of the BCPs.
BLAST
User can query for similar sequences present in ClotBase. The sequence should be pasted in FASTA format. User- defined parameters include E-value, type of alignment and the scoring matrix.
Reference:
Altschul, S. F. et al. (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.
FASTA format
FASTA format for sequences begins with a single-line description of the sequence followed by the sequence. The description line is demarked from the sequence by a greater-than ('>') symbol in the first column.
For example :-
>gi|148745450|AAI42073| Fibrinogen alpha chain [Bos taurus (cattle) ]
MFSVRDLCLVLSLVGAIKTEDGSDPPSGDFLTEGGGVRGPRLVERQQSACKETGWPFCSD
EDWNTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLFNYQKNSKDSNTLTKNIVELMRGDF
Patterns
Patterns are conserved motifs present in sequences. The patterns in BCPs were identified using BlockMaker (http:// bioinfo.weizmann.ac.il/blocks/blockmkr/www/make_blocks.html) and PRATT (http://www.expasy.org/tools/pratt/).
The patterns present in ClotBase are represented in PROSITE format.
A PROSITE format:-
[AC]-X-V-X(4)-{ED}
The above pattern will be translated as [Ala or Cys] - any - Val - any - any - any - any - {any but Glu or Asp}
Consensus sequence
It is a single sequence representation for a protein family. They were identified using BlockMaker (http://bioinfo. weizmann.ac.il/blocks/blockmkr/www/make_blocks.html).
Screen-Mutation
This tool helps in screening for lethal mutations in the protein sequences. Two modules are available:
Reported: The protein sequence provided by the user is aligned with the corresponding wild-type human BCP sequence as deposited in the SwissProt database. Residues, for which missense mutation/s have been reported in literature and present in the sequence, are highlighted. User can thus detect the presence / absence of known missense mutations in their sequence of interest.
Predicted: The user-defined sequence is aligned with the consensus sequence for the corresponding BCP. The presence of substitutions in the conserved residues and patterns may suggest a lethal mutation in the user-defined sequence.
Submit Data
Researchers can submit new information pertaining to sequence, patterns and mutations found in BCPs using this tool. User can also upload any other relevant information using ‘Other’ sub-section.
Disclaimer
The authors do not assume any responsibility for losses of any kind incurred by use of this database.
User can contact us with queries and suggestions at clotbase@bicnirrh.res.in