BLAST query sequence

To identify the relationship between anew gene or the query sequence and those genes that are already known or stored in public databases and to elucidate the functions the new gene may have, programs in BLAST are usually used see Table 1.1). BLAST provides a similarity search for both nucleotide and protein sequences against genomic sequence information available in the databases see Note 3). 

The BLAST searching output can help users deduce functional and evolutionary information for their query sequences. BLAST can also be used for comparisons in certain categories, such as SNP BLAST and Immunoglobin BLAST (IgBlast). 

Sequence similarity search tools Alignments of the query sequence with databases produce sequence similarity. The BLAST series of programs has variants that will translate DNA databases, translate the input sequence, or both. FASTA provides a similar suite of programs. 

Paste the query sequence and click the Search button. The search result (BLAST against PDB and PS I BLAST againt SCOP) with summary of the search and multiple alignment is returned. 

Lost in the above discussion is an unfortunate truth Even with DP, it takes too long to rigorously align a query sequence to each of the member sequences of a database. Because of this, database search tools seek approximations to the optimal local alignment, negotiating a balance between quality and speed with each comparison. This tradeoff and its implications are central to forthcoming discussion of the database search tool BLAST hosted at NCBI. 

The effect of PSI-BLAST is to attune the scoring scheme to the query, and in practice this may or may not be desirable. On one hand, PSI-BLAST can be very sensitive to remote homology on the other hand, spurious sequences may be included and their scores may become inflated. Previously we used NP 000764 as a BLAST query to identify CYP2E1 homologs now we use NP 000764 to initiate a PSI-BLAST search. The first round of PSI-BLAST yields the same BLAST results... 

GeneFIND uses a multi-level filter system, with MOTIFIND and BLAST (Altschul et al., 1997) as the first-level filters to quickly eliminate query sequences that have very low probabilities of being a family member. After searching through all neural networks, the sequence query is considered as a potential PROSITE family member if it is ranked in the top 3% hits of the corresponding network. 

BLAST and FASTA, and their derivatives, take a sequence as input and compare that sequence to a database of sequences (the search database). A list of sequences which are similar to the query sequence is then produced with a score of how well the sequences match. The search database is usually composed of all the sequences in a database such as SWISS-PROT or GENBANK, and hence the matched sequence in the search database contains information which may be useful in annotating the query sequence. 

Click on the link indicated by H next to the Protein-protein BLAST (blastp) to access a similar problem to determine the type of protein. Use the query sequence provided in the problem. This sequence was generated by translating a 4 exon gene from Drosophila. To determine the nature of this protein, run a blastp search against the Swissprot database as described in Subheading 2. The protein is similar to a number of phosphoglucomutases. 

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