Searching databases of conserved sequence regions by aligning protein multiple-alignments [published erratum appears in Nucleic Acids Res 1996 Nov 1;24(21):4372]

Pietrokovski, Shmuel

doi:10.1093/nar/24.19.3836

Cited by 213 publications

(198 citation statements)

References 70 publications

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“…Pairs of ungapped alignment blocks were compared for establishing the significance of their similarities using LAMA [16]. This method allows estimation of the number of blocks (E &!!! )…”

Section: Methodsmentioning

confidence: 99%

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Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction

Ponting

2000

Biochemical Journal

113

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Sequence database searches, using iterative-profile and Hidden-Markov-model approaches, were used to detect hitherto-undetected homologues of proteins that regulate the endoplasmic reticulum (ER)-associated degradation pathway. The translocon-associated subunit Sec63p (Sec = secretory) was shown to contain a domain of unknown function found twice in several Brr2p-like RNA helicases (Brr2 = bad response to refrigeration 2). Additionally, Cue1p (Cue=coupling of ubiquitin conjugation to ER degradation), a yeast protein that recruits the ubiquitin-conjugating (UBC) enzyme Ubc7p to an ER-associated complex, was found to be one of a large family of putative scaffolding-domain-containing proteins that include the autocrine motility factor receptor and fungal Vps9p (Vps=vacuolar protein sorting). Two other yeast translocon-associated molecules, Sec72p and Hrd3p (Hrd = 3-hydroxy-3-methylglutaryl-CoA reductase degradation), were shown to contain multiple tetratricopeptide-repeat-like sequences. From this observation it is suggested that Sec72p associates with a heat-shock protein, Hsp70, in a manner analogous to that known for Hop (Hsp70/Hsp90 organizing protein). Finally, the luminal portion of Ire1p (Ire=high inositol-requiring), thought to convey the sensing function of this transmembrane kinase and endoribonuclease, was shown to contain repeats similar to those in β-propeller proteins. This finding hints at the mechanism by which Ire1p may sense extended unfolded proteins at the expense of compact folded molecules.

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“…Pairs of ungapped alignment blocks were compared for establishing the significance of their similarities using LAMA [16]. This method allows estimation of the number of blocks (E &!!! )…”

Section: Methodsmentioning

confidence: 99%

“…Groups I and II CUE domains were found to be significantly similar when compared using local alignment of multiple alignments (LAMA) [16] …”

Section: Cue1pmentioning

confidence: 99%

Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction

Ponting

2000

Biochemical Journal

113

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“…Therefore, using the newly discovered group of 12 clarin sequences, we defined novel clarin-specific Blocks motifs. These were subsequently analysed by the Local Alignment of Multiple Alignments (LAMA) method, 46 looking for remote but statistically significant similarities between the clarin Blocks and all others. Two of the clarin Blocks, in and around the first and fourth putative TM domains generated a hit with two of the 4TM proteins Blocks ( Figure 3B,C).…”

Section: Gene Product and Protein Structurementioning

confidence: 99%

USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses

et al. 2002

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Usher syndrome type 3 (USH3) is an autosomal recessive disorder characterised by the association of post-lingual progressive hearing loss, progressive visual loss due to retinitis pigmentosa and variable presence of vestibular dysfunction. Because the previously defined transcripts do not account for all USH3 cases, we performed further analysis and revealed the presence of additional exons embedded in longer human and mouse USH3A transcripts and three novel USH3A mutations. Expression of Ush3a transcripts was localised by whole mount in situ hybridisation to cochlear hair cells and spiral ganglion cells. The full length USH3A transcript encodes clarin-1, a four-transmembrane-domain protein, which defines a novel vertebrate-specific family of three paralogues. Limited sequence homology to stargazin, a cerebellar synapse four-transmembrane-domain protein, suggests a role for clarin-1 in hair cell and photoreceptor cell synapses, as well as a common pathophysiological pathway for different Usher syndromes.

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“…Previous approaches for quantifying PFM similarity include: the average log likelihood ratio method proposed by Wang and Stormo (2003), the Pearson correlation coefficient method described by Pietrokovski (1996) and Hughes et al (2000), and a method recently introduced by .…”

Section: Introductionmentioning

confidence: 99%

Similarity of position frequency matrices for transcription factor binding sites

Schones¹,

Sumazin²,

Zhang³

2004

Bioinformatics

103

107

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Motivation:Transcription-factor binding sites in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices. The ability to compare position frequency matrices representing binding sites is especially important for de novo sequence motif discovery, where it is desirable to compare putative matrices to one another and to known matrices. Results: We describe a position frequency matrix similarity quantification method based on product-multinomial distributions, demonstrate its ability to identify position frequency matrix similarity and show that it has a better false positive to false negative ratio compared to existing methods.We group transcription factor binding site frequency matrices from two libraries into matrix families, and identify the matrices that are common and unique to these libraries. We identify similarities and differences between the skeletal-muscle-specific and non-musclespecific frequency matrices for the binding sites of Mef-2, Myf, Sp-1, SRF and TEF of Wasserman and Fickett (1998). We further identify known frequency matrices and matrix families that are strongly similar to the matrices given by Wasserman and Fickett. We provide methodology and tools to compare and query libraries of frequency matrices for transcription factor binding sites. Availability: Software is available to use over the web at

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Searching databases of conserved sequence regions by aligning protein multiple-alignments [published erratum appears in Nucleic Acids Res 1996 Nov 1;24(21):4372]

Cited by 213 publications

References 70 publications

Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction

Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction

USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses

Similarity of position frequency matrices for transcription factor binding sites

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