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Open Access Highly Accessed Research article

Seq2Ref: a web server to facilitate functional interpretation

Wenlin Li2, Qian Cong2, Lisa N Kinch1 and Nick V Grishin12*

Author Affiliations

1 Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA

2 Department of Biochemistry and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA

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BMC Bioinformatics 2013, 14:30  doi:10.1186/1471-2105-14-30

Published: 28 January 2013

Additional files

Additional file 1: Table S1.:

The benchmark result links of enolase superfamily. The table shows the selected representative proteins for families in enolase superfamily and the webpage links of the server results.

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Additional file 2: Table S2.:

Pairwise BLAST results for proteins located in the operon containing YidD. Five proteins from Escherichia coli are compared with corresponding proteins in Cronobacter turicensis.

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Additional file 3: Figure S1.:

The protein similarity network of YidD homologs produced by CLANS program. Each black dot represents one protein sequence. Red circle and green asterisk represent the query (Cronobacter turicensis hlyA) protein and the experimental studied hit (E. coli YidD), respectively. Edges (lines) show BLAST connections between sequences that have an E-value at least as good as 10−33. Lengths of edges indicate that sequences in tightly clustered groups are relatively more similar to each other than sequences with few and distant connections.

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Additional file 4: Figure S2.:

The workflow of Seq2Ref. The whole process can be divided into homologous reference protein detection (Step 1) and homology evaluation (Step 2). Starting from a query sequence, a BLAST/PSI-BLAST search of the NCBI non-redundant database (NR) is performed (Step 1–1) to detect homologous proteins. Seq2Ref detects the reference protein among these homologous proteins by retrieving and checking the information in NCBI databases (Step 1–2). Orange lines represent the reference proteins among the BLAST result. Sequentially, Reciprocal BLAST (RB) and multiple sequence comparison (MSC) will be performed to evaluate the homologous relationships (Step 2–1). Integrating the statistics calculated above, a rating system will assign scores and rank the reference proteins (Step 2–2).

Format: DOCX Size: 59KB Download file

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