You Can try these.

Annotation of the Sequence

1) Automatically annotate a new genome based on existing patterns and annotations in public or local databases including annotating ORFs as hypothetical genes based on these patterns and queries against NCBI.

2) Annotate sequences with ORFs or predict genes with Glimmer

3) Search for motifs by copying and pasting sequences

4) Similarity based annotations (Using BLAST Seqrch for Homology)

5) Multiple Sequence Alignments

SNP Detection and Variant

1) Identify the effect of variations on protein translations, including those where only the first and third positions in a codon vary

2) Calculate the probability of a SNP being correct

Sequence Prediction

1) DNA translation – Translate and complement alongside your nucleotide sequences. Translate in any frame or all 6 frames at once or just translate the annotation or selection that you're interested in.

2) Consensus Sequence – Predict consensus sequences according to your choice of identity schemes including "consensus by quality" on chromatogram data which chooses the best

3) DNA sequences – Predict identity, read coverage, numerous statistics on base frequencies, residue frequencies, CpG islands and more

4) Protein sequences – Predict molecular weight, isoelectric point, hydrophobicity, transmembrane regions, coiled coil regions, amino acid charge and more

Try using NCBI genome workbench. Check the following link:

http://www.ncbi.nlm.nih.gov/tools/gbench/

You Can try these.

Annotation of the Sequence

1) Automatically annotate a new genome based on existing patterns and annotations in public or local databases including annotating ORFs as hypothetical genes based on these patterns and queries against NCBI.

2) Annotate sequences with ORFs or predict genes with Glimmer

3) Search for motifs by copying and pasting sequences

4) Similarity based annotations (Using BLAST Seqrch for Homology)

5) Multiple Sequence Alignments

SNP Detection and Variant

1) Identify the effect of variations on protein translations, including those where only the first and third positions in a codon vary

2) Calculate the probability of a SNP being correct

Sequence Prediction

1) DNA translation – Translate and complement alongside your nucleotide sequences. Translate in any frame or all 6 frames at once or just translate the annotation or selection that you're interested in.

2) Consensus Sequence – Predict consensus sequences according to your choice of identity schemes including "consensus by quality" on chromatogram data which chooses the best

3) DNA sequences – Predict identity, read coverage, numerous statistics on base frequencies, residue frequencies, CpG islands and more

4) Protein sequences – Predict molecular weight, isoelectric point, hydrophobicity, transmembrane regions, coiled coil regions, amino acid charge and more

its better you go through SMART database where u can submit protein and nucleotide sequence there u can find the domains present in the protein which make u to identify the to which family ur protein is related to 

then go through different  blast parameters to find sequence similarity and structure similarity. 

You already blasted it and have 4 variants with 100% identity?

Go through all 4 variants and check for similarities. Genbank gives you tons of information you need: which organism, the sequences are annotated so you can get information about genes, intron, exon etc., link to aminoacid translation.

Also I would suggest to have a look at the publications where the 4 sequences were published (I hope they are published somewhere).

Hello,

Here is a website made for student to learn about sequence annotation:

http://annotathon.org/?actionjs=rules

If you go below "sequence annotation" you will have links to tools that you can use and also advices for the interpretation of the results.

Delphine

Dear  Ash

First please ask yourself what is unknown here.  Is it the "known unknown?"  Is the gene known with no function or you are completely unaware of the genomic repertoire of the sequence in question?

Start with simple crosschecking the sequence, whether or not the sequence has start ATG sites, protein coded with regions flanking, variants etc. That said, you have a variant that matches to your so called "unknown" region, try checking the bidirectional BLAST approach.  This will ensure you have no pseudogenes and then follow the steps as suggested by revered members here. 

Most important take home message:  Simply finding or getting a 100% matches does NOT mean that your sequence is a match. Double check your annotation.  Use two or more tools and reach consensus.  That is Bioinformatics

Best

Prash 

Hi,

You have an unknown sequence. To predict the genes in the genome with ORF characteristics we can use GLIMMER or FGENESH. I have done the annotation for the virus using the methods. Protein characteristics can be studied using domain-finding predictive softwares such as the SMART program. Phylogenetic analysis of the deduced protein can be conducted using MEGA5.0 program after a multiple-sequence alignment analysis using Clustal W. Homology modeling for the predictive structure can be conducted using Swiss-homology modeling and DaliLite software.

All the best.

After running a BLASTn on NCBI, check for the E-value, 100% Ident etc. of the four variants to check for similarities and thereafter mine for information in Genbank for your entries.