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ClosIndb Home page gives information about ,what is closindb and how it will be helpful for the researchers

" In the past few years, several clostridial genomes have been sequenced which makes clostridium as one of the highly sequenced genera. Presently, complete genome sequence of 48 clostridial species is available in public archives. Unraveling this genomic information has potential implications in clostridial research. In the present study, we have carried out in silico analysis to decipher the genomic information. Subsequently, a webresource, ClosIndb, has been developed which collates the computationally derived information associated to all clostridial genes. It features various aspects of coding regions as well as non-coding regions, such as putative orthologs, physicochemical properties, operons and cis-regulatory elements. It also allows user to retrieve intergenic sequence, amino acid sequence, etc. Further, it gives insight to user to the comparative details of all clostridial proteins across the firmicutes. It is the comprehensive resource for all completely sequenced clostridial genomes and is under constant development. "

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ClosIndb can be accessed in searchable as well as Browsable fashion. To browse select any organism from the drop down which is placed on the top of the left side menu. The screen shot of Table of ORFs for Clostridium acetobutylicum ATCC 824 uid57677 taken as example.

Unique Proteins

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Second link in database is to dig unique and conserved proteins present in different clostridium species.
This link has two separate tabs one for each unique and conserved proteins respectively.
When user click on unique proteins menu item it takes you to Unique.php page where it asks you to select Query and target genomes,
on the successful submission it takes you to confirmation page and then gives you results after confirming parameters
[By default it gives output in protein id format,user can change from PID to Synonym]
The screen shot on right gives you a pictorial understand of doing it.

Conserved Proteins

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When user click on Conserved proteins menu item it takes you to Conserved.php page where it asks you to select Query and target genomes,
on the successful submission it takes you to confirmation page and then gives you results after confirming parameters
[By default it gives output in protein id format,user can change from PID to Synonym]
The screen shot on right gives you a pictorial understand of doing it.

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Third link in database is Reciprocal blast hits for genomes present in database. When user click on this link it takes you to RBBH input for query genome and target genome, and also it gives genes present in the query genome. For results two output format like protein id and synonym is given,
user has to select the output format. Default output format is protein id

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User can retrieve the Physico-chemical Properties of all Clostridial Proteins by Searching under “Physicochemical Properties” link. Input can be ORF-ID, Protein ID or Name for all the proteins of interest of User.once user enter the input it will give all properties in same page.
User can provide any of the keyword like PID,Synonym,Accession ID or Gene Name
Physicochemical Properties that have been calculated for each of the clostridial protein are as follows:

• Amino acid composition(Residue, Number, Mole%,DayhoffSta )
• Molecular Weight in Daltons
• Number of Residues
• Average Residue Weight in Daltons
• Net Charge of Protein
• Isoelectric Point ( pI )
• A280 Molar Extinction Coefficients (reduced & cystine-bridges)
• A280 Extinction Coefficients 1mg/ml (reduced & cystine-bridges)
• Probability of Expressed protein entering into an Inclusion Body ( PEPIB )
• GRAVY ( Hydrpoathy Value )
• Protein Sequence
• Protein Side Chain Properties

In the same page user can find Amino acid sequence and intergenic sequence of the Selected protein

View Motifs/Orthologs

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The other link present in closindb is finding motif/orthologs of user input in clostridium genomes.
The input for this link is given in two format one is by giving any keyword like Gene name,protein id,accession number or Synonym.
It gives results of motifs, orthologs present for query sequence.
The Picture on the right side gives you a pictorial representation.

Search Motifs By Sequence

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This link also works like previous one,but this facilitate the user to search by Sequence.
It gives results of motifs, orthologs present for query sequence.
The Picture on the right side gives you a pictorial representation.

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Clusters of Identical Proteins have been constructed by looking identical sequences of proteins in all Clostridial Organisms. Each of the cluster has Identical Proteins either from same organism it belongs to or rest of the Clostridial organism.

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Other link present in closindb is comparisions of different genomes.It compares clostridium with following four genomes.
1.Clostridia Vs Ureaplasma
2.Clostridia Vs Lactococcus
3.Clostridia Vs oceanobacillus
4.Clostridia Vs Thermoanaerobacter
5.Clostridia Vs Listeria
6.Clostridia Vs Mycoplasma
7.Clostridia Vs Staphylococcus
8.Clostridia Vs Streptococcus
9.Clostridia Vs Bacillus
For each comparision user have to selcet query clostridium genome and target genome for comparision.once user select it ask for conformation and nthen it starts comparision of two genomes and gives results in tabular form with query and target on each side and genes which are present in